(Reuters) -The Federal Deposit Insurance Corporation filed a lawsuit accusing Capital One of paying nearly $100 million less than it should have to help bail out depositors of Silicon Valley Bank and Signature Bank, which both collapsed in 2023.

Capital One was sued on Monday night in the federal court in Alexandria, Virginia, two months after the sixth-largest U.S. commercial bank filed its own lawsuit accusing the FDIC of trying to charge $149.2 million too much.

At issue is whether Capital One underreported its uninsured deposits by excluding a $56 billion position between two subsidiaries from regulatory reports describing the McLean, Virginia-based bank's financial health.

The FDIC uses deposit data when calculating special assessments it charges banks to recoup losses to its deposit insurance fund when banks fail.

Capital One had no immediate comment on Tuesday. The FDIC did not immediately respond to requests for comment.

In its countersuit, the FDIC said that excluding the $56 billion position led Capital One to calculate a $324.84 million special assessment for the two bank failures, not the correct $474.08 million amount. About $99.4 million remains unpaid, the FDIC said.

"There are no time machines when it comes to special assessments, and the subsidiary's funds were deposits held at the bank for which the subsidiary already received the benefit of FDIC deposit insurance," the FDIC said.

Capital One estimated in July it may need to set aside an additional $200 million for the matter.

The FDIC seized Silicon Valley Bank and Signature Bank in March 2023, and estimated last June it would recover $18.6 billion from 111 banks through special assessments.

Banks with less than $5 billion of assets are not charged. The FDIC provides deposit insurance to 4,376 banks and savings associations.

In January, the FDIC sued 17 former Silicon Valley Bank executives and directors in the San Jose, California federal court, seeking billions of dollars for alleged gross negligence and breaches of fiduciary duty. That case remains pending.