"Thank you to the great people of The Villages. The Radical Left Do Nothing Democrats will Fall in the Fall. Corrupt Joe is shot. See you soon!!" he wrote in the tweet. Roughly three hours later, the tweet no longer appeared in Trump's timeline.
"President Trump is a big fan of the Villages. He did not hear the one statement made on the video. What he did see was tremendous enthusiasm from his many supporters," White House deputy press secretary Judd Deere said in a statement.
Before the tweet was deleted, South Carolina Sen. Tim Scott, the only Black senator in the Republican conference, said on Sunday that the video retweeted by the President was offensive and "indefensible."
"There's no question. He should not have retweeted and he should just take it down," Scott said on CNN's "State of the Union" with Jake Tapper.
US Secretary of Health and Human Services Alex Azar told Tapper he hadn't seen the video, which was played on the same news program, or the President's tweet, "but obviously neither the President, his administration nor I would do anything to be supportive of white supremacy or anything that would support discrimination of any kind."
Azar declined to comment further when Tapper asked if it was a mistake by the President. "But obviously the President and I and his whole administration would stand against any acts of white supremacy."
Former national security adviser John Bolton told Tapper on "State of the Union" that it's possible that Trump tweeted the video because he saw a "Trump 2020" sign and had not paid attention.
"It may be that you can draw a conclusion that he heard it, and it was racist, and he tweeted it to promote the message. It is a legitimate conclusion to draw. It is also entirely legitimate to say he just had no idea what else was in the video other than the Trump sign," Bolton said.
Amid nationwide protests over racial injustice and police brutality this month, the President has retrenched into divisive themes instead of seeking a unifying tone.
This story has been updated with additional developments Sunday.
CNN's Manu Raju, Kevin Liptak, Ryan Nobles and Donald Judd contributed to this report.