On September 20, 2012, amid protests against torture and rapes in Georgian prisons, the Ministry of Internal Affairs announced Akhalaia had resigned from office.

In this capacity he led a struggle against the established system of "thieves in law" which ruled prisons in the post-Soviet country, but he was a frequent target of criticism by the opposition, some human rights groups and Public Defender Subari.

The Georgian media ran stories about Akhalaia's alleged tensions with then-Minister Vasil Sikharulidze and Chief of Joint Staff Vladimer Chachibaia.

The vehicle features a V-shaped hull, enhancing protection against landmines and IEDs, with claims suggesting it can withstand a 6 kg mine blast.

However, then president Mikheil Saakashvili pardoned him in November 2013.During his pretrial detention, which endured for a period of 23 months, Akhalaia was acquitted in several cases.

[23] But he could not leave the prison because the pretrial detention was added to other cases[24][25][26][27][28] in 2013 The first acquittal of Akhalaia in the court was followed by sharp reactions in the ruling team, the Georgian Dream Democratic Coalition's protest was left by the People's Party Chairman Koba Davitashvili.

[29][30][31][32][33][28] When commenting on the acquittal, Gedevan Popkhadze, a member of the parliament from the ruling party, made the following comment to the media: “Whether he will be acquitted or not, Bacho Akhalaia should still be in prison.”[34] Parliamentary Assembly of Council of Europe (PACE) adopted a resolution criticizing Georgia, along with Turkey and Russia, for “abuse of pretrial detention, the resolution brings an example of former Tbilisi Mayor Gigi Ugulava and ex-defense minister Bacho Akhalaia.

According to the prosecutor, on January 12, 2006, the officers of Constitutional Security Department shot three young people with an unprecedented brutality near the Navtlughi bus terminal.

Bachana Akhalaia, who was a high-ranking government official at that time, ordered and directly participated in severely torturing six inmates in order to get from them a favourable testimony that murdered people were planning an armed attack on prison for the purpose of a mass escape of prisoners.Regarding this case, Akhalaia's lawyer Malkhaz velijanashvili, stated that this is a completely illegal and unsubstantiated verdict, there was no evidence in the case.

The book delves into the dynamics of occupied territories and the prevailing socio-political situation in the country in prison he also translated several notable books, including "The Art of War" by Martin Van Creveld, "Supreme Command" by Eliot Cohen, "Why Nations Fail" by Daron Acemoglu and James Robinson, and "Crises" by Henry Kissinger.

"Truth About the Mafia” by Judge Giovanni Falcone, Currently he is actively engaged in producing the first Georgian translation and commentary of Carl von Clausewitz's "On War.