WASHINGTON — Federal contactors complained on Thursday that they were being given short shrift by guidelines released by the intelligence community for paying employees with coronavirus relief funds.

The guidelines from the Office of the Director of National Intelligence allow intelligence agencies to fund contractors for lost hours from March 27, the date President Trump signed the $2 trillion relief package into law. But federal contractors say the rules are far more restrictive than the Pentagon’s guidelines, which allow relief from losses the companies began to suffer starting at the end of January, when a national emergency was declared.

Because many of the nation’s intelligence agencies, like the Defense Intelligence Agency and the National Security Agency, are part of the military, it is not clear which set of rules applies.

At stake are millions of dollars to help intelligence contractors recover from losses in recent weeks, when their workers with top-secret clearances have been blocked from going to work. Because they work with classified material, which generally can be viewed only in secured rooms or on secured electronic systems, they have been unable to perform their jobs, putting the contracts at risk.