JPMorgan, which acquired Washington Mutual from the FDIC for $1.9 billion at the height of the financial crisis, has disputed its responsibility to cover losses incurred by investors on the failed thrift's mortgage securities.
Reuters reported exclusively on Sept. 30 that the dispute threatened the preliminary deal.
The Department of Justice has sought a provision in the settlement that prohibits JPMorgan from seeking to push the WaMu liabilities from the settlement onto the FDIC.
The bank has not yet agreed to such a provision, one of the people familiar with the talks said. Talks have not yet broken down over the disagreements and negotiations are continuing, the person added.
$23 billion war chest
JPMorgan chief executive Jamie Dimon has sought to put liabilities stemming from the 2007-2009 financial crisis behind the bank.
For Dimon, a delay or breakdown in the negotiations would put him further away from showing investors and employees that he can end the expense and damage to the bank's reputation caused by the litigation.
(Read more: The truth about that awful JPMorgan settlement)
The largest U.S. bank said it set aside $23 billion earlier this month to pay for legal issues, and will continues to face more than a dozen government investigations globally, even after it puts the mortgage probes behind it.
The Justice Department alone is investigating the bank for everything from bad derivative bets, to whether it gave jobs to the children of government officials in China to secure business there, to whether it played a role in the manipulation of Libor benchmark interest rates.
The DOJ has led negotiations to resolve multiple state and federal probes into JPMorgan's mortgage bond business and that of the firms it acquired during the financial crisis.
On Friday, one of the agencies, the Federal Housing Finance Agency, grew impatient waiting for the completion of the package and separately signed a $5.1 billion settlement with JPMorgan. Some $4 billion of that had been seen as counting toward the $13 billion amount.
(Read more: JPMorgan in $5.1 billion deal with housing agency)
Dimon met with U.S. Attorney General Eric Holder in late September in Washington to reach the tentative package deal.
Holder and Dimon are both overseas this week. Holder is in Morocco attending a conference and meeting with local counterparts. Dimon is traveling in Europe this week, according to a person familiar with his itinerary.