JPMorgan Chase’s chief executive Jamie Dimon made it clear that the bank vows to fight the Federal Deposit Insurance Corp. to shoulder losses on mortgage securities sold by Washington Mutual to private investors. ( Jim Young/Reuters)

As part of its $13 billion settlement with the government this week, JPMorgan Chase agreed to abandon a bid to have the Federal Deposit Insurance Corp. absorb some of the losses on faulty mortgage securities sold by Washington Mutual, the failed bank it bought out of receivership five years ago.

But that’s only part of the fight.

The question of who bears responsibility for WaMu’s legal liabilities has been a point of contention since JPMorgan scooped the bank out of receivership in 2008. JPMorgan argues that the FDIC agreed to take on some of those liabilities, a claim the agency denies.

Tensions flared up during negotiations between the Justice Department and JPMorgan as the bank wanted the FDIC to handle the costs of the defective WaMu securities involved in the government’s complaint. The disagreement almost scuttled the landmark pact before JPMorgan backed off.

But in a call with analysts Tuesday, JPMorgan chief executive Jamie Dimon made clear that the battle with the FDIC is not over.

“We have the right to go against the receiver,” Dimon told analysts. “If it takes five years, we’re fine with that.”

Dimon’s statement arose out of a question about a dispute with 21 asset managers, pension funds and insurance funds that invested in residential mortgage-backed securities trusts issued by JPMorgan, its Bear Stearns unit and WaMu.

Last week, the institutional investors reached a $4.5 billion deal to settle claims tied to JPMorgan and Bear Stearns, but the agreement did not cover any WaMu securities. That’s because JPMorgan is still needling the FDIC to absorb those liabilities, Dimon said on the call.

Banks such as JPMorgan and WaMu bundled hundreds of home loans into securities and marketed them as investments that could be traded like stocks. When millions of homeowners defaulted on their mortgages and the housing market collapsed, the value of the securities took a nose dive and investors were saddled with huge losses.

Several investors have sued both JPMorgan and the FDIC for damages from WaMu’s alleged breach of contract over mortgages pooled into securities.

One of the largest cases involves Deutsche Bank National Trust, which filed a lawsuit in 2010 asking either the bank or the regulator to cough up $6 billion to $10 billion for low-quality mortgages in WaMu securities. In a court filing, JPMorgan insisted that it never assumed any liability for the claims in Deutsche Bank’s case.

JPMorgan contends that the money left over from the receivership process should cover investor claims. The $2.7 billion left in that fund is supposed to cover claims from WaMu creditors, who have been waiting for five years to be paid.

“Whatever remains in the receivership, which has a lot of cash, will be paid out to bondholders,” Dimon reiterated during the call. “We have the full right on all WaMu, which includes the Deutsche Bank thing, to go after the receiver . . . and we intend to do it.”

Officials at the FDIC declined to comment on ongoing litigation.

Analysts following the dispute between JPMorgan and the FDIC say it is difficult to resolve. The agreement the bank signed when it picked up WaMu was never clear about who is responsible for violations of securitization agreements, wrote John McDonald, a Sanford C. Bernstein analyst, in a research report.

Some observers insist the liabilities lie with the bank — period.

“The preponderance of evidence of the deal documents makes it clear that they are fighting over loopholes in a scorched-earth strategy, rather than intending to follow the spirit of an acquisition that has provided them phenomenal returns,” said Joshua Rosner, managing director of the research firm Graham Fisher & Co.

There is some chance the Justice settlement could bolster the FDIC’s position in the ongoing private litigation, said Andrew Stoltman, a securities lawyer.

“I don’t think there is any question that the FDIC would argue that JPMorgan has unclean hands in this process,” he said. “JPMorgan does have an argument that it shouldn’t be responsible because it had nothing to do with the activity. The flip side of that argument is that if you get the benefit, you get the liabilities.”

For the FDIC, the $13 billion JPMorgan deal is a bittersweet victory. On the one hand, it is no closer to ending the saga over the private WaMu litigation. On the other, the FDIC does not have the headache of battling JPMorgan over millions of dollars in losses suffered by investors, such as Fannie Mae and Freddie Mac. Plus, the agency received $515.4 million out of the settlement to resolve 10 securities lawsuits against JPMorgan filed on behalf of five failed banks.