Labor Secretary William E. Brock, in a dramatic speech to the International Brotherhood of Teamsters convention, today called on the nation's largest union to "clean house" in the cases where criminal interests have dominated the union.

Flanked by Teamster President Jackie Presser, who was indicted Friday after an investigation initiated by the Labor Department, Brock delivered a surprise call for reform within the 1.6 million-member union, whose leaders have strongly backed the Reagan administration.

"As secretary of labor, it isn't easy to hear about mobbed-up locals, or pension fund abuse -- misuse of members' blood and sweat. It's impossible for me to ignore that. It is necessary for you to address it," Brock told 2,000 Teamster officials at the opening of the union's convention, held every five years.

"As a national organization, you've lost a great deal of public trust," Brock continued. "And you need to ask yourselves those hard questions -- beginning with the hardest question: Why?"

The President's Commission on Organized Crime has described Presser as the latest of three Teamster presidents with links to organized crime. Brock did not mention Presser by name, and he drew a standing ovation from the delegates when he said that anyone under suspicion must be presumed innocent until proven guilty.

But Brock, addressing a crowd consisting overwhelmingly of Presser loyalists, said they must examine whether some of the 700 Teamster locals are places "where crime interests reign and members' interests are ignored or trampled. If there are such locals, put them in trusteeship.

"Are there areas where good people have been silent too long, where it's just plain time to clean house? If so, do it."

Brock's unexpectedly strong speech contrasted sharply with the upbeat political greetings delivered to the Teamsters today by Vice President Bush, former secretary of state Alexander M. Haig Jr., Republican National Committee Chairman Frank J. Fahrenkopf Jr., Democratic National Committee Chairman Paul G. Kirk Jr. and others who either appeared in person or sent videotaped messages of praise for the union and appreciation for its political support.

Bush, who reportedly angered Presser by declining an invitation to speak here, recorded a four-minute video in which he mistakenly congratulated the Teamsters for membership growth.

"You can take pride," Bush said, that while other unions have declined, "your union continues to grow."

The Teamsters have lost more than 300,000 members in the last five years, largely because deregulation has led to the closing of hundreds of unionized trucking firms. Overall, membership losses have far outpaced the Teamsters' gains of thousands of public-sector and health-care workers.

Brock's speech was also a marked contrast with the last address by a labor secretary to the Teamsters. That occurred in 1976 when William J. Usery embraced Teamster chief Frank Fitzsimmons and declared an alliance between the union and Republicans.

Brock, a former Republican Party chairman, compared the Teamsters to the Republicans just after Watergate, saying that the public mistakenly believed that the entire GOP was "rotten."

"You've got some of the same problems today," Brock said. "You can't ignore them . . . . As secretary of labor, I can't ignore them either, and I won't."

Brock, whose bluntness drew applause from the delegates, left the convention hall immediately after his speech, declining to answer questions.

In his address, Brock said that in recent days he had been urged to cancel his appearance before the Teamsters, but he said he did not because it would have implied that he believes Presser is guilty of charges that he made payments of $700,000 to "ghost employes" who did no work for the union.

Presser was greeted by tumultuous ovations as he opened the union's convention, declaring himself "proud to be a Teamster" and later stating his innocence of the racketeering and embezzlement charges.

"I stand before you today as I have stood my entire career," Presser said, flashing a thumbs-up sign to the delegates and about 3,000 guests before him at the Las Vegas Convention Center. "I am proud to be a Teamster."

"The government's five-year investigation has been a farce," Presser said, blaming prosecutors and the media for his troubles. "The charges . . . are political and false . . . and designed to embarrass the working men and women of our great international union."

"It proves the government has been out to get me at any cost," he said.

To rid the Teamsters of criminal influence, union reformers have suggested that the Labor Department challenge the Teamsters' election method. Union members do not vote directly for national officers, nor do they have final say in the selection of most of the 2,000 delegates who do the voting.

Brock has asked his department, which previously declined to challenge the election methods, to restudy the process, but he did not mention elections in his speech.

Outside the convention hall, about 100 dissident Teamsters picketed and flew a 12-foot-long blimp carrying a message protesting the lack of direct elections for union officers.

Inside, however, local Teamster officers among the delegates said in interviews that they strongly support Presser, describing him as the victim of government harassment and politically motivated prosecution. Presser is expected to be elected to a five-year term Wednesday.