Cole linked the discrepancy to the alleged wrongdoing by a former NRCC treasurer, Christopher J. Ward, whom members have accused of forging multiple financial audits during his time as the committee's top bookkeeper.
Cole met with leaders early this afternoon, shortly before he sat down with members of his own executive committee to update lawmakers on the progress of an internal investigation.
House Republican leader John A. Boehner (Ohio) acknowledged in an interview with Politico Wednesday that the amount of money missing could exceed previously reported sums in the hundreds of thousands of dollars, saying party leaders do not yet know the full extent of those losses.
Roll Call first reported this most recent discrepancy on its website.
The FEC could require the campaign committee to pay fines for misreporting its fundraising totals, but the commission has also established guidelines to avoid those additional penalties.
Ronald C. Machen, an attorney with WilmerHale representing Ward, did not immediately respond to an e-mail for comment.