Reinstated from the 15-day disabled list after missing the previous 59 games because of a torn ligament in his left thumb, Harper openly questioned Williams' decisions hours before the team's 7-3 victory over the Colorado Rockies in Washington.
The manager's lineup included Ryan Zimmerman at third base, Anthony Rendon at second base, Harper in left field and second baseman Danny Espinosa on the bench.
"I think [Zimmerman] should be playing left. Rendon's a good third baseman. He should be playing third. We've got one of the best second basemen in the league in Danny Espinosa," Harper told reporters. "Of course, we want the best-hitting lineup in there. [But] I think Rendon playing third and Zim playing left is something that would be good for this team. I think that should be what's happening."
Harper, 21, previously has said he "loves" playing center field and hoped to be there when he came off the DL. So playing in left in his first game back could have caused some of the apparent dissatisfaction.
"I haven't talked to nobody about anything, so I have no clue," he said. "I know I'm playing left tonight, via Twitter. So I guess that's where I'm going."
Williams, when told of Harper's comments before the game, took the high road.
"Happy to have him back," the first-year Nationals manager told reporters. "When he's out there, regardless of where he's at, we'd like him to catch it when it's hit to him and hit it when it's thrown to him. ... I don't have any comment other than that. ... Hopefully, I can write his name in there every single day the rest of the year. That would be very important."
Williams echoed a similar sentiment when asked about Harper's comments on Tuesday.
"I've got to let you guys know something: I've got Bryce's back in everywhere. That will not change," he said before Washington's home game versus Colorado. "I know there is a lot made of it and a lot of discussion about it, but he and I are good. There is no rift. We have a conversation every day. I support him all the way. I'm happy to write his name in the lineup every day. Who wouldn't be."
Harper also batted sixth Monday night, a spot where he had seen part-time duty before the injury but also one outside the heart of the order. He went 1 for 3 with a run scored. Williams is expected to use the same lineup Tuesday night.
Williams said Tuesday that he spoke with Harper about his lineup comments.
"I want him to play every day and I want him to play the way Bryce knows how to play. He's going to hit in different spots in the lineup. He's OK with that. He's going to play in different spots in the outfield and he's OK with that too."
Zimmerman, whose chronic shoulder problems had moved him off third base, had been playing in Harper's spot in left field.
Information from The Associated Press was used in this report.
Nationals Win In Harper's Return
Bryce Harper scored one run and had one RBI in the Nationals' 7-3 win over the Rockies.