The organization had been hopeful Chen was close to rejoining the rotation, but now, his status is in limbo.
"Chen didn't go as good as we'd [have] liked today," manager Don Mattingly said. "We'll still see where that goes. ... I expected it to be good after his bullpen [Wednesday]. The next day was good. Today, we are in a holding pattern with Wei-Yin."
Chen threw about 15-20 pitches off the mound on Saturday before he was shut down. He is dealing with discomfort in his left elbow.
For a while, Chen has been pitching through a slight ulnar collateral ligament tear. Until his setback, he was managing pitching with the tear.
"He was feeling something again," Mattingly said.
The Marlins signed Chen to a five-year, $80 million contract in January 2016, and he missed nearly two months last season due to a left elbow sprain.
Chen is off to a 2-1 start with a 4.33 ERA this year, making five starts and throwing 27 innings. The lefty's best game of the season came on April 18 at Seattle, when he threw seven no-hit innings and finished with 100 pitches.
Miami had a combined no-hit bid broken up that night in the ninth inning.
In Chen's past start, he worked six innings, giving up two runs at Tampa Bay. He finished with 96 pitches.
According to Statcast™, Chen's fastball average for that game was 90.8 mph. His maximum velocity in the game was 92.6 mph and his low was 88.4 mph. For the season, his fastball average is 90.92 mph, so his velocity was consistent in his most recent start.
The Marlins announced lefty Justin Nicolino, who was at Triple-A New Orleans and also is on the 40-man roster, as their starter for Sunday.
Because of Thursday's off-day, Miami had the option of moving up Dan Straily to pitch on Sunday, and Tom Koehler on Monday. Instead, Mattingly said Straily will stay on Monday and Koehler on Tuesday against Houston.
The Marlins did make a roster move on Saturday, reinstating Edinson Volquez from the disabled list. Hard-throwing reliever Brian Ellington was optioned to New Orleans. Volquez had been out with a right thumb blister.
Had Chen's bullpen gone without incident, he could have been a possibility to start on Tuesday. For now, he may get another MRI, and more on his status will be known in the upcoming days.
"We don't have a scheduled start or a rehab for him right now," Mattingly said.
Joe Frisaro has covered the Marlins for MLB.com since 2002. Follow him on Twitter @JoeFrisaro and listen to his podcast. This story was not subject to the approval of Major League Baseball or its clubs.