"I want to extend my sincere apologies to those in our Scouting family who were offended by the political rhetoric that was inserted into the jamboree," said Chief Scout Executive Michael Surbaugh. "That was never our intent."
Speaking Monday before about 40,000 Scouts, Trump delivered a speech that would not have been out of place on his campaign or in his tweets.
He slammed the "fake news" media, promoted the repeal of the Affordable Care Act, boasted about his election night victory and called out the Washington "cesspool."
"Who the hell wants to speak about politics when I'm in front of the Boy Scouts," he said, continuing to speak about politics.
Trump also riffed on the Boy Scouts loyalty pledge to criticize those in Washington.
"We could really use some more loyalty, I will tell you that," Trump said.
The speech represented a marked change from prior presidential speeches to the Boy Scouts, which generally discussed values and service rather than partisan issues. A number of former Scouts criticized the nakedly partisan speech, and CNN contributor and retired Lt. Gen. Mark Hertling said the President "did not provide the proper example" to the crowd of young men.
In his letter, Surbaugh said Trump's speech had overshadowed the rest of the jamboree and its focus on Scouting.
"These character-building experiences have not diminished in recent days at the jamboree -- Scouts have continued to trade patches, climb rock walls, and share stories about the day's adventures," he said. "But for our Scouting family at home not able to see these real moments of Scouting, we know the past few days have been overshadowed by the remarks offered by the President of the United States."
Surbaugh said the invitation to the sitting President to visit the Jamboree is a "longstanding tradition" dating to 1937.
"It is in no way an endorsement of any person, party or policies," Surbaugh said. "For years, people have called upon us to take a position on political issues, and we have steadfastly remained nonpartisan and refused to comment on political matters. We sincerely regret that politics were inserted into the Scouting program.
"While we live in a challenging time in a country divided along political lines, the focus of Scouting remains the same today as every day," he said.
At the press briefing on Thursday, White House press secretary Sarah Huckabee Sanders said she had not seen the letter yet. She said from her firsthand view the Jamboree was "one of the most energetic crowds" she has seen for Trump.
"I was at that event and I saw nothing but roughly 40-45,000 Boy Scouts cheering the President on throughout his remarks," she said. "I think they were pretty excited that he was there and happy to hear him speak to them."
CNN's Allie Malloy contributed to this report.