Nationals manager Davey Johnson said he knew Harper likely would not play against the Atlanta Braves when he saw him limp off the team's charter flight.
"It's bothering him," Johnson said. "We've got to try to figure out whether he needs more rest or what we have to do to get him by that."
Harper said on Thursday in Baltimore that he hoped to return against Atlanta, but Johnson doubts the 20-year-old will play this weekend.
The Nationals might consider putting Harper on the disabled list, but Johnson said they could wait until Tuesday when right fielder Jayson Werth is supposed to return from a rehab assignment.