"All we are doing is giving them a bit of education and what goes on" in the due diligence process, Johnson said of his company's dealings with investigators.
The office of New York State Attorney General Andrew Cuomo had no immediate comment. In March, Cuomo said that his office was examining the subprime mortgage market.
Clayton is one of the nation's largest due-diligence companies hired by investment houses to make sure that blocks of loans conform to the seller's own standards. Investment houses may decide to either accept or reject a due-diligence company's opinion on the quality of mortgage loans.
Johnson said Wall Street firms relaxed their guidelines for due diligence companies during the recent housing boom, which allowed millions of subprime borrowers to win loans despite their shaky credit history.
"We were hired by the buyer. They can say 'I am buying these, or not,"' he said. "In hindsight, we got away from the roots which is saying 'This is a good loan that is going to pay and this is a bad loan."'
During the height of the housing boom, investment houses often disregarded the views of their due-diligence firms and bought baskets of mortgages despite warnings because they did not want to lose business, other due-diligence executives said.
"Twelve months ago there was a lot of competition for newly originated loans and the buyer who would purchase more of the pool was more likely to win that bid. The choices sometimes were business choices," said Bruce Watterson, the president of Watterson Prime of Bellevue, Wash. Watterson Prime is owned by Fidelity National Information Services, Watterson said.
Watterson said he has not been contacted by investigators.