A police officer in India's Gujarat state says the government there authorised the killing of Muslims three years ago.
The state government of Narendra Modi denies the allegations
RB Sreekumar made the allegation in notes he kept at the time while serving as Gujarat's intelligence chief.
The Gujarat government says the charges are baseless and untrue, instigated because Mr Sreekumar was not promoted.
Officially more than 1,000 people, most of them Muslims, died in religious riots in Gujarat in 2002.
Human rights groups say many more were killed.
Mr Sreekumar was appointed intelligence chief in April, 2002. Sporadic violence was still occurring in Gujarat then, after the worst of the rioting in February and March.
His allegations relate to his dealings with the Gujarat government after his appointment.
The Gujarat government issued a statement on Thursday denying the charges, saying they had "no veracity".
Mr Sreekumar has submitted his notes to India Central Administrative Tribunal (CAT) which investigates complaints by civil servants.
He brought a case against the Gujarat government, saying he was denied a promotion for refusing to act upon the "illegal and unconstitutional directives" of Gujarat Chief Minister Narendra Modi as well as the state government and senior state police officers.
The Gujarat riots of 2002 left at least 1,000 people dead
Mr Modi has been criticised for his handling of the riots at home and abroad.
In the notes, Mr Sreekumar alleges that the chief minister asked him to tap the telephones of Shankersinh Vaghela, who was then president of the Congress party.
He said that he was also asked to tap the telephone of cabinet minister Haren Pandya.
In the notes, Mr Sreekumar also says that senior government officials sent messages asking him to kill Muslim extremists who were involved in rioting.
He alleges that the state police chief told him in May 2002 that Gujarat's most senior civil servant had spoken about "eliminating those Muslim extremists who are disturbing the communal peace of Ahmedabad".
Mr Modi has wide support among Hindu nationalists
The city is Gujarat's commercial centre.
In an entry in June 2002, Mr Sreekumar wrote that a senior civil servant, G Subba Rao had told him to "eliminate" any person trying to disrupt a Hindu religious event in the state.
"He (Mr Rao) added that this is the well considered decision of Chief Minister Narendra Modi," Mr Sreekumar wrote.
He further claims that when he informed Mr Subba Rao that such "elimination" was illegal, he was told that "such action can be taken on situational logic".
In another entry in May 2002, Mr Sreekumar wrote that Narendra Modi asked him to concentrate on suspected Muslim militants as hardline Hindu activists are "not doing anything illegal".
He also alleges in his petition that state government lawyers tried to "tutor him" before he submitted his deposition to the commission.
Mr Sreekumar's lawyer Anand Yagnik told the BBC that the tribunal had issued notices to Mr Modi and other government officials requesting them to reply by 9 May to the allegations.