CBS News' Stephanie Lambidakis confirmed that the FBI is investigating the failed bank and that the probe began before its collapse.
The investigation is focused on the company - which was taken over last Friday by the FDIC - and not individuals who ran it, according to a law enforcement official who was not authorized to speak publicly about the investigation.
IndyMac Bank's assets were seized by federal regulators after the mortgage lender succumbed to the pressures of tighter credit, tumbling home prices and rising foreclosures.
The bank is the largest regulated thrift to fail and the second largest financial institution to close in U.S. history, regulators said.
"The FBI currently has 21 investigations related to the sub-prime market industry," FBI spokesman Richard Kolko told CBS News. "We receive information from a variety of sources on a daily basis, and we have an obligation to review each allegation on its merits. Given the volatility of today's subprime market, we have seen an increase in sub-prime related complaints."
The Office of Thrift Supervision said it transferred IndyMac's operations to the Federal Deposit Insurance Corporation because it did not think the lender could meet its depositors' demands.
FDIC spokesman David Barr could not immediately be reached for comment Wednesday.
Over the last year, and faced with a cratering housing market, the FBI has opened a wide-ranging probe of companies across the financial services industry, from mortgage lenders to investment banks that bundle home loans into securities sold to investors.
Countrywide Financial Corp., the nation's largest mortgage lender, is also under scrutiny.
Additionally, two former Bears Stearns managers were indicted last month on conspiracy and securities and wire fraud charges alleging they lied to investors in a hedge fund that tanked last year as the subprime market collapsed. Those charges marked the first criminal charges to arise on Wall Street from the subprime mortgage debacle.