Mr. Pane, who acknowledged his past legal problems, said on Saturday that they had no bearing on his work as an employee for Bio-Recovery. The revelations were first reported by BuzzFeed. Though Mr. Pane is listed as the operator of the company on Environmental Protection Agency records, he said he had no ownership stake in the company and that his role included technical and public relations responsibilities.

Mr. Pane said he changed the spelling of his surname to Pain, but the E.P.A. records and court papers filed by Mr. Cuomo’s office related to the fraud charges use only Pane. Officials with Comptroller Scott M. Stringer’s office said on Saturday that because the cleanup contract for Dr. Spencer’s apartment was handled on an emergency basis, the city’s request was reviewed only preliminarily before the work began. The comptroller’s office gave prior approval for the cleanup work, for up to $500,000, and was aware that Bio-Recovery would do the work. Eric Sumberg, a spokesman for the comptroller’s office, said in a statement on Saturday: “This office has no tolerance for corruption. When we receive this contract for registration we will take all steps necessary to ensure that this vendor has the integrity to do business with the city.”

A spokesman for Mayor Bill de Blasio, Phil Walzak, said that city health officials inspected Dr. Spencer’s apartment after the cleanup and reviewed the company’s waste disposal practices. He said that all work was found to have been safely completed.

Messages left at Bio-Recovery on Saturday were not returned.

Though Bio-Recovery has done about 10 jobs for the city in the last six years, Mr. Walzak said, its work has been limited enough that it reported only basic business information to the city. Mr. Pane’s name is not in the city’s vetting system, Mr. Walzak said.