The NFL released a statement saying "a small number of clubs" had been penalized by having space under their salary caps taken away due to contracts they signed in 2010 that pushed spending into an uncapped year.
The clubs included Washington, which will lose $36 million of salary cap space, and Dallas, which will lose $10 million, ESPN.com reported.
NFL.com said teams were warned not to push spending into the uncapped year as a way getting around future salary caps. But the NFL Network said the Cowboys and Redskins deny going against the policy.
"The Dallas Cowboys were in compliance with all league salary cap rules during the uncapped year," the Cowboys' said in a statement. "We look forward to the start of the free-agency period where our commitment to improving our team remains unchanged."
Redskins General Manager Bruce Allen said the club had received "no written documentation from the NFL concerning adjustments to the team salary cap in 2012 as reported in various media outlets."
"Every contract entered into by the club during the applicable periods complied with the 2010 and 2011 collective bargaining agreements and, in fact, were approved by the NFL commissioner's office," Allen said.
The penalties came as the NFL prepared to open its free-agency season Tuesday.
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