Alfred S. Regnery, President Reagan's nominee to head the Justice Department's Office of Juvenile Justice and Delinquency Prevention, was confirmed yesterday by the Senate on a 69-to-28 vote. Democrats cast all but two of the negative votes.

Regnery, a former aide to Sen. Paul Laxalt (R-Nev.) and a former official of Young Americans for Freedom, had been a controversial nominee because of his intention to shift some funding away from preventing delinquency and toward stiffer punishments for juveniles who commit serious crimes. Some opponents also have charged that he is inexperienced in the juvenile justice field.

The nomination was put on hold briefly while the White House asked the FBI to investigate charges by a Madison pediatrician that Regnery posed "a danger to the health needs of our children." Because of medical ethics, the doctor refused to elaborate except to say that his charge was based on Regnery's behavior during the 1975 birth of one of his children in Madison.

The FBI report has not been released, but Democratic and Republican senators who have seen it said it does not contain information relevant to Regnery's confirmation.

The nomination of Regnery, who moved to Juvenile Justice on an acting basis last year from his former job as deputy assistant attorney general in the Lands and Natural Resources Division, was debated for an hour, with Sen. William Proxmire (D-Wis.) saying, "There is nothing in his background to qualify him for the post."

Conceding that Regnery is not experienced in juvenile justice, Laxalt said experience is "desirable but not indispensible. Sometimes I think we're overloaded with experts . . . . After all, he has practice. He has four wonderful children."

Sen. Howard M. Metzenbaum (D-Ohio) retorted, "On that basis, the father of eight children would be doubly qualified. I can find no qualifications, none whatsoever, other than what 10 or 20 million other Americans might have."