Police said they were Lashkar-e-Taiba (LeT) terrorists and were conspiring to kill Chief Minister Narendra Modi.
The home ministry had filed an affidavit in the Supreme Court, maintaining that the four had links with the LeT.
Ahmedabad's Metropolitan Magistrate S.P. Tamang's probe report released Monday asserted there was no shootout between the four and the police. The report said the four were students and had been kidnapped from Mumbai June 12, 2004, and killed two days later.
Facing criticism after the probe report, the Gujaart government had pointed out that the home ministry had claimed the four were terrorists.
Chidambaram said: 'If a state government acts as though intelligence inputs are evidence or conclusive proof, I am sorry for that government.
'Certainly no one suggested that based on an intelligence input you should kill someone. I think too much is being attributed to that affidavit... if it is meant to defend the government of Gujarat against the excesses that may have been committed by its police. I am sorry for the government of Gujarat and the manner in which it runs its police administration,' he said while speaking out for the first time on the controversial affidavit.
Chidambaram was visiting the US for four days since Tuesday.