Top officials of the nation's third-largest waste disposal company, testifying under oath before a congressional hearing yesterday, denied allegations that the company has ties to organized crime and has engaged in anticompetitive practices.

But a New Jersey law enforcement official indicated in testimony that a state investigation involving similar allegations and looking at patterns of bids in northern New Jersey by SCA Services Inc. is continuing.

Allegations about SCA surfaced before the same House subcommittee December 16, 1980. Ex-convict and FBI informant Harold Kaufman testified before the subcommittee on oversight and investigations that the waste disposal industry in New Jersey is controlled by organized crime, which he said was extending its influence into toxic waste disposal.

According to Kaufman, waste disposal companies divide up lucrative collection routes by a system of property rights granting certain routes to certain companies. The system is enforced by organized crime, according to that testimony and state and federal investigators. Kaufman, who is in the federal witness protection program, had also testified concerning alleged ties between organized crime and SCA, through subsidiaries the firm had acquired in New Jersey.

SCA operates several major hazardous waste facilities and serves commercial and residential customers in 32 states and the District of Columbia. Shayne Brothers Inc. in this area is an SCA subsidiary.

"I deny, under oath, categorically and without qualifications, each and every allegation made against me and my company," SCA President Tom Viola told the House subcommittee on oversight and investigations. Viola called charges made by ex-convict Harold Kaufman unsubstantiated lies and produced a copy of a letter from the FBI that said, "there is no record that . . . Viola has been the subject of an investigation by the FBI."

Viola was accompanied by SCA Board of Directors Chairman John M. Fox, who is also a director of IBM and a former president of the Minute Maid Corporation. Fox testified that the board of directors had appointed a special committee that retained attorneys to conduct an investigation into Kaufman's charges, which were made to the same subcommittee last December. "The investigation has revealed, I can report, either that there is no evidence to support Mr. Kaufman's allegations, or that they are demonstrably false or incredible," he said.

However, later Fox said that the investigation is continuing and that it had not included charges made yesterday by both New Jersey state police and FBI officials that the manager of an SCA subsidiary in New Jersey was an associate of organized crime figures and worked with them to settle disputes over waste disposal contracts.

The subsidiary manager, Crescent Roselle, was shot to death on Dec. 22, 1980 in a still-unsolved slaying.

Allegations about ties between SCA employes and organized crime center on New Jersey subsidiaries acquired by the firm in the 1970s.

FBI information "contains indications that Mr. Roselle was an associate of organized crime figures and acted on their behalf," testified Wayne Comer, supervisor of the FBI's Newark office. Comer told the committee that when SCA purchased firms such as Rosell's, control remained in local hands. "As a result the respect for 'property rights' and the contact with or co-existence with organized crime, which predated SCA, continued."