The Senate approved the nomination of Alex Kozinski yesterday to be a federal appeals court judge, although with the highest negative vote it has ever delivered against one of President Reagan's nominees.

Kozinski won confirmation on a 54-to-43 vote that reflected a spate of allegations by some critics and former employes that Kozinski's temperament made him unsuited for the federal bench.

Kozinski, 35, chief judge of the U.S. Court of Claims, will be the youngest federal appellate judge in the nation when he joins the 9th U.S. Circuit Court of Appeals in California.

Three Republicans -- Sens. Barry Goldwater (Ariz.), Lowell P. Weicker Jr. (Conn.) and William S. Cohen (Maine) -- joined 40 Democrats in opposing the conservative nominee.

Kozinski, a Romanian immigrant, said yesterday that he was "very pleased, relieved and grateful to be confirmed."

He said the support that he has received from his friends "makes all the pain worthwhile."

"I understand the concerns of the negative votes . . . . I'll work very hard to make everyone who voted for me proud of having cast the vote," Kozinski said.

Sen. Carl Levin (D-Mich.), who led the opposition, said that the narrow margin of the vote "sends a message that the American people want judges who, whatever their other qualifications, can be counted on to treat people fairly, decently and forthrightly."

The Senate Judiciary Committee held an unusual second hearing on Kozinski last week after it had cleared the nomination.

The panel examined affidavits from several former employes who described Kozinski as an abusive boss who mistreated his employes when he headed the Merit Systems Protection Board's Office of Special Counsel in 1981 and 1982.

Kozinski's former press secretary said that Kozinski had barred her from talking to other employes or reporters.

Another former employe said he was humiliated when Kozinski made him repair office furniture.

Some charged that Kozinski had mishandled key cases and misrepresented his record to the committee.

Kozinski denied the allegations, and three other former aides praised his tenure at the special counsel's office.

Kozinski also was sharply criticized for distributing a radio broadcast editorial that supported his nomination and accused his leading critic, the Government Accountability Project, of having ties to terrorist groups.

Kozinski said he did not endorse all the statements in the editorial.