Mitch McConnell, the senate Republican leader, defended Mukasey, saying: "Tonight, a clear bipartisan majority of the US senate voted to confirm Judge Mukasey because he is one of the most qualified candidates ever nominated to the position of attorney general".
Mukasey had been given initial support from senators who saw him as a fair and independent-minded nominee.
But the former judge was criticsed after he told the senate judiciary committee at his confirmation hearing last month that torture violated the US constitution, but he was unsure if waterboarding was unlawful.
In a follow-up letter Mukasey said that he finds waterboarding "repugnant", but would be unable to determine its legality until he examined classified US interrogation policies.
Harry Reid, the senate Democratic leader, expressed doubts concerning Mukasey: "Judge Mukasey's answer to the waterboarding question was important in itself, but it also raised for me serious doubts about whether he is prepared to be the truly independent voice that the justice department so desperately needs.
"If he cannot stand up to the president on such a question of profound importance with a clear legal answer, how can we be sure that he would be more than just another mouthpiece for an administration that treasures secrecy and loyalty above all?" Reid asked.
Mukasey's confirmation promises included the enforcement of any new laws that specifically bans waterboarding.