The Justice Department says several lenders caught up in long-running mortgage securities investigations had dragged out the government’s work by failing to cooperate and have only themselves to blame for the “cloud of uncertainty” that hung over them.

Bill Baer, the department’s No. 3 official, used a speech Tuesday in Chicago to recount the “stunning breakdown of ethics” and compliance among banks that packaged and sold faulty residential mortgage bonds at the heart of the 2008 financial crisis. Without help from the banks in several instances, he said, the government was forced to build cases from the ground up.

“Each prolonged the period in which a cloud of uncertainty hung over the institution. And each paid a lot more than it would have if it had cooperated early on,” Baer said.

Investors are monitoring the Justice Department for signals on how it’s handling negotiations with Deutsche Bank to settle inquiries into the lender’s residential mortgage-backed securities operation. The U.S. opened settlement talks with a request for a $14 billion penalty, the bank has said. That’s more than the bank, which also has yet to resolve U.S. investigations into foreign-currency rigging and precious metals trading, says it’s willing to pay.

Deutsche Bank, which didn’t have a comment on Baer’s remarks, reiterated that its settlement negotiations had just begun and that it “expects an outcome similar to those of peer banks, which have settled at materially lower amounts.”

Baer didn’t discuss pending investigations. But as investors, analysts and shareholders ask how much Germany’s biggest bank can afford to pay, he placed the onus for delayed settlements and high penalties on banks’ general response to investigators, referring to five firms that have already reached $46 billion in civil mortgage-related settlements.

“Whether to cooperate with the government in these matters is a choice companies need to make,” Baer said. The banks under investigation “chose not to,” he said.

The government’s focus on mortgage bonds stems from a working group of prosecutors and other officials that President Obama created in 2012 to punish Wall Street for fueling the financial crisis by selling bonds linked to souring mortgages. The Justice Department had been pilloried for years for not having brought significant cases against banks and their executives.

The banks that already settled claims over their mortgage dealings are JPMorgan Chase & Co., Citigroup Inc., Bank of America Corp., Morgan Stanley and Goldman Sachs Group Inc. In addition to Deutsche Bank, the banks that have yet to settle with the Justice Department are Credit Suisse Group AG, UBS Group AG, Royal Bank of Scotland Group Plc, HSBC Holdings Plc and Barclays Plc, all of which have disclosed U.S. investigations into mortgage securities dealings.