Tuesday also marks the first day of the free agency negotiating period before the start of free agency on Thursday.
The Washington Post first reported the news. Redskins spokesman Tony Wyllie told NFL.com, "We're busy with free agency," when asked about McCloughan's whereabouts.
"He is not in the building today for free agency at all," Rapoport reported on Free Agency Frenzy on Tuesday. "When agents are taking calls from Redskins, and there have been some, it is from from Eric Schaffer (vice president of football administration)."
Rapoport said McCloughan was running draft meetings for the team last week, according to sources. He added that people with the Redskins were surprised to learn McCloughan was not in Indianapolis for the combine after they arrived.
"Now we learn that he's not involved in free agency," Rapoport said. "It's pretty safe to say the future of Scot McCloughan is very much in doubt in Washington."
McCloughan's absence comes at one of the busiest times of the year for NFL general managers and front offices. Like many teams, the Redskins are expected to be active in free agency. They have roughly $34 million in room to work with under the $167 million salary cap, according to Overthecap.com.