A Brooklyn rabbi pleaded guilty yesterday to paying more than $5,000 in bribes to Rep. Daniel J. Flood (D-Pa.) for the congressman's help in obtaining federal contracts for his Jewish poverty agency.

Rabbi Leib Pinter, 34, head of B'Nai Torah Institute in New York, told a federal judge in Manhattan that he paid Flood about $1,000 at least five times between late 1974 and early 1976.

"I made payments to Congressman Flood to use his influence in his official capacity as a congressman," Pinter said. "I asked him and a member of his staff to use their official capacity to intercede with various government agencies on behalf of myself and my organization."

Flood, chairman of the Appropriations subcommittee that funds all Labor and Health, Education and Welfare Department programs, issued a statement denying the charges.

But Pinter's guilty plea to the bribery charge and his appearance as a grand jury witness against the congressman focus attention again on the flamboyant 74-year-old Flood.

Flood's activities have been the subject of federal grand jury investigations in several cities since his long-time top aide, Stephen B. Elko, turned government witness and alleged that his former boss had traded his influence for more than $100,000 in cash.

The alleged payments from Pinter to Flood have been mentioned before by Elko. But the rabbi's guilty plea - he faces a possible 15-year prison term on the bribery charge - is the first time someone has admitted criminal guilt in making payments directly to Flood.

Pinter also agreed to plead guilty to tax charges in Brooklyn and to defrauding a government summer lunch program in Philadelphia.

The bribery charge states specifically that Pinter bribed Flood to increase appropriations for a jobs program for the elderly, to write a leter to Rep. Otto E. Passman (D-La.) making a request, and to influence Labor Department officials' consideration of Pinter's proposals.

Funding fro the jobs program for the elderly has increased by millions of dollars each year, but B'nai Torah Institute has never been granted a contract.

The non-profit institute has received several other grants since its founding in 1972, however. B'Nai Torah got slightly less than $2 million in 1975 and 1976 for a program to train Jewish immigrants from the Soviet Union in English and job skills, according to a Labor Department spokesman.

And the institute received $3.5 million in 1975 and $6.2 million in 1976 for running a summer luch program in the New York area for the Department of Agriculture, sources familiar with the investigation said yesterday.

That program was expanded to Chicago, Philadelphia and New Jersey in 1976. B'Nai Torah's operation of the program in New York and Philadelphia has been under investigation forisome time.

The Washington Post reported in February that Flood had received $1,000 in campaign contributions and an honorarium from Pinter and his institute.

In December 1975, after the contract for aiding Soviet immigrants had been approved, B'Nai Torah honored Flood with its public service award.