The contractor that the Giuliani administration selected 13 years ago to help rid the Fulton Fish Market of corruption is now facing criminal charges, with prosecutors alleging it stole from the Port Authority of New York and New Jersey.

In the mid-1990s, Laro Maintenance Corp. and its owner, Robert Bertuglia, stepped into the spotlight after winning a contract to unload fish at the lower Manhattan market, where refrigerated tractor-trailers bearing catches from across the Eastern seaboard converged. Amid demonstrations and police guard, Laro took over the work from the six unloading companies that the Giuliani administration had ousted from the fish market. Officials had said that the market was ensnared in organized crime and that the unloaders were known to demand inflated prices for unloading fish fast enough to prevent spoiling, according to news articles from the time.

Laro, a large contractor for janitorial services that had no experience in unloading seafood at the time, unloaded fish until the market moved in 2005 to an indoor facility in the Hunts Point section of the South Bronx.

In an indictment unsealed yesterday, prosecutors from the office of the Manhattan district attorney, Robert Morgenthau, charged both Laro and Mr. Bertuglia with submitting inflated bills as part of its contract to provide janitors to clean the Port Authority Bus Terminal. The company and its owner are accused of submitting invoices for more than $200,000 worth of cleaning equipment that was never actually purchased, according to a press release from the district attorney’s office.

Mr. Bertuglia, 53, pleaded not guilty in court yesterday, his attorney, Gino Josh Singer, said in an interview.

“We believe the charges have no merit and that when all the facts are made known he will be found not guilty,” Mr. Singer said.

The lawyer said the Port Authority has complimented Laro on its work in the past and in January renewed the bus station contract with the company for another three years. The previous three-year contract was worth $24 million, Mr. Singer said, noting that the amount at issue in the charges is less than 1% of its value.

Mr. Bertuglia and his company are charged with grand larceny and falsifying business records.

A former chief of staff to Mr. Giuliani, Randy Mastro, who oversaw the effort at the fish market, declined to comment, saying he was unfamiliar with the charges.