"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," Michael Surbaugh, chief scout executive for the Boy Scouts, said in a statement.
"That was never our intent."
Trump addressed tens of thousands of boy scouts at their National Jamboree in West Virginia on Monday night, delivering a highly partisan speech that has been widely criticized.
The Boy Scouts organization's Facebook page was deluged Tuesday with comments critical of the president's appearance.
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Surbaugh, in his statement, said it is a long-standing tradition to invite the sitting US president to visit the scouting 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.
"We sincerely regret that politics were inserted into the Scouting program," he said.