A violent coup in Tbilisi, which ousted President Gamsakhurdia in favor of the interim Military Council from December 20, 1991 to January 6, 1992, marked the start of the civil war in Georgia. Gamsakhurdia fled Georgia, but his armed supporters continued their resistance to the new regime, especially in Mingrelia (Samegrelo), and enjoyed significant support among the Georgian population in Abkhazia. In March 1992, the Military Council was transformed into the State Council of the Republic of Georgia led by the ethnic Georgian ex-Foreign Minister of the Soviet Union, Eduard Shevardnadze.
Once again, tensions began to fuel in Abkhazia. The Abkhaz separatist politicians led by Ardzinba were determined to use the opportunity of the unrest in Georgia to reinforce their power in the region and not to allow either of the conflicting Georgian parties to gain a foothold in Abkhazia. In violation of the previous power-sharing agreement, the Abkhaz team gradually began to take control of all major posts in the autonomous structures. An internal division within the Georgian faction did not allow the Georgians to effectively counter these moves. By summer 1992, the split-up in the local authorities and public institutions of Abkhazia into ethnic Georgian and ethnic Abkhaz groups created a kind of dual authority in the autonomous republic. The predominantly ethnic Georgian members of the Supreme Council – the “Democratic Abkhazia” faction headed by Tamaz Nadareishvili – blamed Ardzinba and his team for raising ethnic tensions in the region and boycotted the Council’s sessions. In the aftermath, a number of Georgian laws were nullified in Abkhazia and a paramilitary force, the Abkhaz National Guard, was created and placed directly under the command of the Presidium of the Abkhazian Supreme Council. The ethnic Georgians responded to these measures by requesting from the central Georgian government to take additional measures for their defense. Soon a Georgian National Guard detachment under the command of Colonel Giorgi Karkarashvili entered Abkhazia and proceeded to the northern border with Russia, but the unprepared Abkhaz militias avoided offering any resistance and the Georgian force left the region. This demonstration of force proved to be ineffective, however. In a counter-move, on June 24, 1992, the Abkhaz National Guard, under orders from Ardzinba, stormed the Abkhazian Interior Ministry office, which was headed by ethnic Georgians, and took control of local police and security units. At the same time, the Abkhaz separatists secured the assistance from the Confederation in the case of an armed conflict, and intensified their contacts with the Russian military leaders and hardliner politicians. Prior to that, Ardzinba had arranged for the redeployment of a Russian Airborne battalion from the Baltic States to Sokhumi. According to the Russian historian Svetlana Chervonnaya, a number of Russian security servicemen arrived in Abkhazia as "tourists" during that summer. According to another Russian expert, Evgeni Kozhokin, director of the Russian Institute of Strategic Studies, prior to the outbreak of hostilities, Abkhaz guardsmen had been supplied with weaponry by Russia’s 643rd anti-aircraft missile regiment and a military unit stationed in Gudauta, Abkhazia. Ardzinba had major supporters in Moscow as well, particularly among the hardliner right-wing circles, including Vice President Alexander Rutskoy and the Chechen speaker of the Russian State Duma, Ruslan Khasbulatov. It should also be noted, that just before the conflict, Georgia also received its limited share of the heritage of the former Soviet military under the Tashkent Agreement of May 15 1992.
At the same time, Ardzinba’s rhetoric mounted, as he claimed that Abkhazia would ready to fight Georgia. In the breach of the 1990 agreement, he initiated a practice of replacing ethnic Georgian officials with Abkhaz, frequently accompanied by violence and humiliation.
On July 23, 1992, the ethnic Abkhaz members of the Supreme Council – twenty eight of the sixty-five deputies - abrogated Abkhazia's functioning constitution and restored the 1925 constitution of the Abkhazian SSR. Abkhazia proclaimed itself a sovereign state, the Republic of Abkhazia, and declared its intention to conduct its relations with Georgia on the parity basis. The Georgian government condemned the decision and Abkhazia's Georgian population went on strike. The region was on the verge of the war.
On August 14, 1992, some 3,000 Georgian National Guard troops and police forces under Tengiz Kitovani entered Abkhazia, their official purpose being the protection of rail communications from Gamsakhurdia’s supporters operating in the region and gain the release of several Georgian governmental officials, including Deputy Prime Minister Alexander Kavsadze, who had been detained by the deposed president’s forces. Abkhaz leaders claimed this was in violation of the agreement of April 1992 whereby Georgian troops could enter Abkhazia with the permission of the Abkhazian government. Although the local Abkhazian authorities had already disintegrated, Shevardnadze still informed Ardzinba about the forthcoming "anti-terrorist operation." However, when Kitovani’s force moved to Sokhumi, the Abkhaz National Guards offered resistance, firing on the Georgian echelons at Ochamchire and Sokhumi. The Abkhaz militias were defeated and they engaged into a scattered guerilla actions. The Georgian forces entered Sokhumi and marched up to the Russian border, forcing the separatist government to leave, on August 18, Sokhumi for Gudauta, which was a home to the Soviet-era Russian military base. Ardzinba declared Gudauta Abkhazia's "temporary capital" and called in the North Caucasian Confederates to interfere.
The Abkhazians' military defeat was met with a hostile response by the self-styled Confederation of Mountain Peoples of the Caucasus, an umbrella group uniting a number of pro-Russian movements in the North Caucasus, Russia (Chechens, Cossacks, Ossetians and others). Hundreds of volunteer paramilitaries from Russia (including the then little known Shamil Basayev) joined forces with the Abkhazian separatists to fight the Georgian government forces. Regular Russian forces also reportedly sided with the secessionsts. In September, the Abkhaz and Russian paramilitaries mounted a major offensive after breaking a cease-fire, which drove the Georgian forces out of large swathes of the republic. Shevardnadze's government accused Russia of giving covert military support to the rebels with the aim of "detaching from Georgia its native territory and the Georgia-Russian frontier land". The year 1992 ended with the rebels in control of much of Abkhazia northwest of Sokhumi.
In March 1993, the anti-Georgian coalition forces launched mass offensive against Georgian-held Sokhumi, accompanied by heavy civilian casualties. The attackers were actively supported by the regular Russian navy and aviation. The Russian Defense Minister Grachev claimed that the Georgians bombed themselves in order to cast a shadow on Russian military. Shortly after this absurd statement, Georgian army brought down a Russian jet piloted by Major Shipko of Russian Air Force, a fact that was confirmed by international observers who investigated the incident. The March offensive turned a disaster to the separatists and their allies. The Georgian artillery destroyed their major military group at the Gumista River. The Abkhaz-North Caucasian forces exhausted and faced an imminent catastrophe. However, under Msocow’s strong pressure Georgian government was forced to sign a truce.
The conflict remained stalemated until July 1993, when the Abkhaz separatist militias launched yet another abortive attack on Sokhumi. The capital was surrounded and heavily shelled, with Shevardnadze himself trapped in the city. Although the Georgian army retained control of the city, the situation was very dangerous as many of the surrounding settlements had been captured by the Abkhaz.
Although a truce was declared at the end of July, this collapsed after a renewed Abkhaz attack in mid-September. Most of Georgian hardware, under the Russian supervision, had already been withdrawn from Sokhumi, and the defenders of the city found themselves undermanned. At the same time, all equipment ceded by the Abkhaz militants to the Russian mission as part of the ceasefire accord, were returned back to the separatists. After ten days of heavy fighting, Sokhumi fell on 27 September, 1993. Eduard Shevardnadze narrowly escaped death, having vowed to stay in the city no matter what, but he was eventually forced to flee when separatist snipers fired on the hotel where he was residing. Abkhaz, North Caucasians militants and their allies committed one of the most horrific massacres of this war against remaining Georgian civilians in the city known as Sokhumi Massacre. The mass killings and destruction continued for two weeks, leaving thousands dead and missing.
The separatist forces quickly overran the rest of Abkhazia as the Georgian government faced a second threat: an uprising by the supporters of the deposed Zviad Gamsakhurdia in the region of Mingrelia (Samegrelo). In the chaotic aftermath of defeat almost all ethnic Georgian population fled the region by sea or over the mountains escaping a large-scale ethnic cleansing initiated by the victors. Many thousands died — it is estimated that between 10,000-30,000 ethnic Georgians and 3,000 ethnic Abkhaz may have perished — and some 250,000 people were forced into exile.
During the war, gross human rights violations were reported on the both sides (see Human Rights Watch report), and the ethnic cleansing committed by the Abkhaz forces and their allies is recognised by the Organization for Security and Cooperation in Europe (OSCE) Summits in Budapest (1994), Lisbon (1996) and Istanbul (1999)