In a tweet, the president called McCaskill "phony" and claimed "people are really upset" about her use of the plane. Trump also endorsed McCaskill's expected opponent in her November bid for re-election, state Attorney General Josh Hawley.
Trump's jab adds to the political blowback the senator is facing for the story during a critical re-election campaign. McCaskill's seat is one of the top Republican targets in this year's midterms. She faces re-election in a state Trump won by nearly 20 points in 2016.
The election is among a handful that will help to determine whether Republicans can defend or expand their 51 to 49 seat Senate majority in November.
McCaskill's campaign did not immediately respond to a request to comment on Trump's tweet.
On Tuesday, McCaskill confirmed that she used a plane for part of the three-day tour. She said she "spent two-plus days on the RV," calling the plane narrative "election-year silliness," according to Politico.
Republicans have latched on to her use of a private plane. Hawley called McCaskill "out of touch." Senate Republicans' campaign arm also has highlighted the story repeatedly since Tuesday.
Polling in the race between McCaskill and Hawley so far has found a slight edge for the incumbent senator, according to a RealClearPolitics average.