The Labor Department moved yesterday to strengthen management of its controversial jobs program and disclosed some audit figures to refute critics' allegations of widespread fraud and waste.

Officials said that department audits of $5.5 billion in spending under the Comprehensive Employment and Training Act (CETA) over the last five years show $34 million in misspent money, roughly one-half of 1 percent.

While this is considerably less than some congressional and other critics have suggested, Labor Secretary Ray Marshall acknowledged room for improvement by naming Charles B. Knapp, a trusted personal aide, to take charge of the nearly $10 billion CETA program.

Knapp, a 32-year-old economics professor who was an associate of Marshall at the University of Texas before joining his personal staff here in 1977, will serve in a new post of deputy to Assistant Secretaty Ernest Green, who is in overall charge of employment and training.

Knapp told reporters he will strive for better management and cooridination of the employment and training programs, along with smoother relations with Congress where CETA has been threatened with new cutbacks this year.

While acknowledging there have been abuses of the program, Knapp said exaggerations have obscured the program's achievements in reducing unemployment and training people for jobs.

The audits, conducted by department officials over the past four years, have reviewed about 400 of 460 CETA project sponsors dating back to 1974 and found about $120 million in "questionable" expenditures, according to department officials. Of the $120 million, $34 million was found to be spent improperly, they said, and efforts are under way to recover it. The other $86 million is under review.