Akhtar, a leader of the Muttahida Qaumi Movement-Pakistan, appeared in court today along with the other accused.
The accused could not be indicted in the other cases related to the May 12 violence owing to the absence of legal counsels.
However, the court indicted them in one case and summoned witnesses to record their statements at the next hearing.
The hearing was then adjourned until June 23.
Talking to the media after the hearing, Akhtar, who served as the home adviser when the May 12, 2007 violence took place, said there should be impartial investigations into the real perpetrators of violence.
Calling for an end to fake cases, the mayor said they are not the one to run away and will face the courts.
Akhtar recalled that after becoming mayor of Karachi, he was nominated in dozens of cases against him as part of a political vendetta.
On May 12, 2007, around 50 people were killed and hundreds injured as clashes broke out in the city between rival political groups after a visit of then-chief justice of Pakistan Iftikhar Mohammad Chaudhry.
Akhtar was elected mayor of Karachi in August 2016 while he was in jail on judicial remand in various cases.