The three investigations were among the first to weigh criminal charges against the companies and executives at the heart of the housing crisis, which was in part caused by offering so-called sub-prime loans to people who may not have otherwise qualified for credit.
The U.S. Attorney's office in Los Angeles, which initiated the IndyMac and New Century probes, could not be reached for comment.
The Justice Department, in a statement dated on Friday, said its investigation closed after hundreds of interviews and review of millions of documents related to WaMu's operations and subsequent failure. The evidence did not meet the standards for criminal charges, the statement said.
The three lenders were overwhelmed by bad loans during the housing crisis. IndyMac and WaMu were seized by federal regulators in 2008 and New Century collapsed into bankruptcy in 2007.
Investigators have struggled to prove intentional wrongdoing, which is required to secure a conviction, particularly in relation to decisions signed off by in-house lawyers, the newspaper said, citing its sources.