The apology came in a statement from chief scout executive Michael Surbaugh, three days after Mr Trump’s speech to nearly 40,000 scouts and adults gathered in West Virginia.
Other US presidents have delivered non-political speeches at past jamborees, but to the dismay of many parents and former scouts, Republican Mr Trump promoted his political agenda and derided his rivals.
His comments led to some of the scouts in attendance booing at the mention of his predecessor Barack Obama.
“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,” Mr Surbaugh said. “That was never our intent… We sincerely regret that politics were inserted into the scouting programme.”
Mr Surbaugh noted that every sitting president since 1937 has been invited to visit the jamboree.
“It is in no way an endorsement of any person, party or policies,” he said. “For years, people have called upon us to take a position on political issues, and we have steadfastly remained non-partisan and refused to comment on political matters.”
Mr Surbaugh contended that the Trump controversy has not diminished the success of the 10-day jamboree, yet he acknowledged its impact.
“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.”
Mr Surbaugh’s statement echoed some of the sentiments expressed by the Boy Scouts’ president Randall Stephenson on Wednesday.
Mr Stephenson said Boy Scout leaders anticipated Mr Trump would spark controversy with a politically tinged speech, yet felt obliged to invite him out of respect for his office.
Hoping to minimise friction, the Boy Scouts issued guidelines to adult staff members for how the audience should react to the speech. Any type of political chanting was specifically discouraged.
But Mr Stephenson, who was not in attendance at Mr Trump’s speech, said the guidance was not followed impeccably.
“There were some areas where perhaps they were not in compliance with what we instructed,” he said. “There’s probably criticism that could be levelled.”
Mr Stephenson was asked whether the Scouts would invite Mr Trump back to address the next national jamboree if he wins re-election.
“I don’t see why we would break with tradition, whoever is holding office,” he said.
“We are not to going to censor or edit the president of the United States. That’s beyond our pay grade, regardless of who it is.”