He became Chief of General Staff of the Georgian military and First Deputy Defense Minister of Georgia after the overthrow of President Zviad Gamsakhurdia in January 1992.
With Georgia descending into chaos of a civil war and military collapse, Tskitishvili, with his Russian counterpart General Mikhail Kolesnikov signed in Moscow, on 9 October 1993, a Russian-Georgian treaty, granting to Russia several key military bases and facilities in Georgia.
In December 1993, Brigadier General Tskitishvili resigned as a reaction to the military setback in Abkhazia and he was succeeded by Major-General Guram Nikolaishvili.
In 1996 he resumed military service, being promoted to the rank of major-general and appointed chief of staff of the border forces.
He returned to state service once again in 2013 and was appointed adviser to the head of Department of Veteran Affairs of the General Staff of the Georgian Armed Forces.