Israeli police chief Moshe Karadi has resigned after a government commission into alleged misconduct by the police said he should leave the job.
Mr Karadi was departmental head at the time of the killing
Mr Karadi insisted he had done nothing wrong but wanted to set an example.
The commission said he should be removed for failing to make sure that the police thoroughly investigated the 1999 murder of a suspected crime boss.
He is also said to have ignored links between senior officers and leading figures within criminal circles.
Mr Karadi was not police commissioner at the time of the killing, but a departmental head.
The suspected crime boss was murdered by a policeman while in hospital under police guard.
The officer, who was later arrested for another offence, said he was acting on the orders of a well-known Israeli crime family.
After he made the confession he escaped to Mexico and was himself murdered. The case was later closed by police due to a lack of evidence.
The commission was formed to determine whether the closure of the case had been appropriate.
Tax Authority head Jackie Matza also resigned on Sunday amid allegations that appointments were influenced by powerful businessmen in exchange for tax breaks.
The resignations are the latest in a series of unconnected but damaging scandals involving senior figures within the Israeli establishment.
President Moshe Katsav is facing allegations that he raped an employee in his office and the police are investigating Prime Minister Ehud Olmert's financial affairs.