But when asked whether FEGS had been contacted by criminal investigators at the Manhattan district attorney’s office or by the state attorney general’s office, Ms. Farber declined to comment. Officials at those offices also declined to comment.

Image Steven Banks, commissioner of the city’s Human Resources Administration. Credit... Victor J. Blue for The New York Times

So what do we know? FEGS reported operating losses two years in a row, according to the agency’s tax returns from fiscal years 2011 and 2012, the most recent returns publicly available.

Thirty percent of FEGS’s budget went toward administrative costs, including salaries, which is considerably higher than most watchdog groups recommend. In fiscal year 2012, Gail Magaliff, the previous chief executive officer, earned a base salary of $482,436, plus additional compensation of $156,444, for a package of $638,880, the tax return shows.

(In New York, nonprofits that receive state funding can use that money to pay executive salaries of up to $199,000, though agencies are not barred from using different funding sources to cover higher salaries and administrative costs. In April, the law will also preclude state funds from covering administrative costs that exceed 15 percent of the budget.)

And there is more: The agency had leases for offices it did not need. FEGS also counted money that it expected to receive from the government as money it had actually received, and it lacked adequate financial controls and computer systems to make that disparity clear, according to government officials and others who have become familiar with the agency’s accounting in recent months.

Although the agency had long prided itself on its professionalism, it was not meeting some of the performance milestones required in city contracts, failing to evaluate some clients in a timely manner, place them in jobs or sign them up for disability benefits, officials say.