WASHINGTON – The Senate voted unanimously yesterday to confirm Judge Michael Chertoff as the second secretary of homeland security, after he pledged in his confirmation hearing to uphold civil liberties while protecting the nation from terrorists.

Senators from both parties praised the former prosecutor and senior Justice Department official for giving up a recent lifetime position as a federal appellate court judge to take the reins of the sprawling bureaucracy. The vote was 98 to 0.

Judge Chertoff, 51, assured both of New York’s senators personally that he would seek more federal homeland security money to the state, the senators said.

Senator Clinton had cast a lone vote against Judge Chertoff’s confirmation on two previous occasions on account of his past role as chief counsel to the Senate Whitewater Committee that investigated a failed Arkansas real-estate deal that involved the Clintons.

Mrs. Clinton has said she opposed his appointment as the head of the Justice Department’s criminal division, and to the U.S. Court of Appeals for the Third Circuit, to protest his treatment of junior White House staffers during the Whitewater hearings.

Yesterday she showed no sign of personal pique as she endorsed him to run the sprawling, 2-year-old department that consolidated 22 departments and 180,000 employees.

“After rigorous review of Judge Chertoff’s testimony and my personal discussion with him, I have come to the conclusion that Judge Chertoff is professionally qualified to be Secretary of Homeland Security and that he understands and respects the values that the Secretary works to defend,” Mrs. Clinton said in a statement.

The senator praised what she called Judge Chertoff’s “stated commitment” to distributing federal homeland security funds based on threat – a formula that is expected to benefit New York City – and his support for “policies that are essential to the security of New Yorkers.”

The Empire State’s senior senator, Senator Schumer, also praised the nominee, noting that he and Judge Chertoff met in person and discussed the funding needs for the city and the upstate border with Canada.

“Judge Chertoff assured me that he would fight within the administration for the resources that have been missing in homeland security,” Mr. Schumer said.

New Yorkers in Congress have complained that New York gets $5.47 a person in homeland security funds, while Wyoming receives $38.31 a person.

“Judge Chertoff assured me that he would look at this funding formula to make sure that New York received the most possible funding because it is among the top terrorist targets in the world, Mr. Schumer said.

Mr. Schumer also praised Judge Chertoff as having the “skill and intelligence” to run the department.

The Senate’s vote was delayed as Democrats sought in vain to obtain additional documents from the administration to shed light on the nominee’s role in developing policy on the treatment of detainees.

The senior Democrat on the Judiciary Committee, Senator Leahy of Vermont, voted in favor of the nomination, but said he was “concerned” that Judge Chertoff had not been “more assertive” during discussions with the White House Office of Legal Counsel as it promulgated a policy that narrowed the definition of torture. The policy was later changed.

During his confirmation hearings, Judge Chertoff pledged to safeguard civil liberties and condemned torture. He also acknowledged that while he was head of the Justice Department’s investigations after the September 11, 2001, attacks, officials had mishandled the detention of hundreds of noncitizens of Arab and South Asian descent, many of whom were held for months without charges or access to a lawyer.

The government should learn from its mistakes, he said.

Judge Chertoff is Mr. Bush’s second candidate to replace Mr. Ridge. A former New York police commissioner, Bernard Kerik, withdrew his name, citing concerns that he had not paid Social Security taxes for a foreign domestic worker.

Born in Elizabeth, N.J., Judge Chertoff is the son of a rabbi. He graduated from Harvard College and Harvard Law School. During his early career, he was a clerk for Supreme Court Justice Brennan and prosecuted mafia and political corruption in the Manhattan U.S. Attorney’s office under a former mayor, Rudolph Giuliani.

Christopher Anders, a legislative counsel for the American Civil Liberties Union, which has criticized some of the administration’s policies in the war on terror, said that “while his record may have some troubling points of concern, we look forward to finding common ground with the agency that impacts the lives of so many.”

The ACLU yesterday said the appointment to the Cabinet of two individuals with ties to the administration’s detention policies highlights the need for an independent counsel to investigate and prosecute any acts by civilians that contributed to the abuse of prisoners in American custody.