The right-hander is scheduled for surgery Friday to remove bone chips from his pitching elbow. He's expected to be sidelined until August.
"If there are spurs or other things in there, it might perhaps take a little longer for the recovery," Nationals general manager Mike Rizzo said Wednesday after his team's 6-4 victory over the New York Mets.
Marquis made a rehab start for Class A Potomac on Tuesday night and said his ailing right elbow stiffened "pretty bad" when he woke up Wednesday morning.
"Not much range of motion," he said. "Not where I want to be. Not what I expected coming into this season. I wanted to help this organization get back on track, but they're doing a great job of it right now."
An All-Star in 2009, Marquis joined the Nationals as a free agent in the offseason, signing a $15 million, two-year contract after going 15-13 with a 4.04 ERA for the Colorado Rockies last season.
He went 0-3 with a 20.52 ERA in three starts for Washington before going on the 15-day disabled list last month with inflammation in his elbow caused by bone chips.
"It's disappointing, but it's part of the game. It's part of the grind that we go through," he said. "Hopefully we caught it where there's no further damage. ... Clean up and be back to hopefully help down the stretch."
Asked whether the Nationals could have saved time by going ahead with the operation weeks ago, Rizzo said: "It was an agreement between the team and the player. He felt he could pitch through it. It set us back about three weeks."
The 31-year-old Marquis, who grew up in New York, was in the Washington clubhouse before the finale of a three-game series at Citi Field. He said he's never had surgery on his arm before.
"If that's what has to be done to get me right and be Jason Marquis again, then I guess that's something I have to do," he said. "I'm surely not the first to have surgery and I'm definitely not going to be the last."
Marquis threw 216 innings last season, surpassing 200 for the third time in his career, and made his first All-Star team thanks to a strong first half.