The puppeteer who performs as Elmo on Sesame Street is taking a leave of absence from the popular children's show over allegations he had a relationship with a 16-year-old boy.

Sesame Workshop said puppeteer Kevin Clash denies the accusations, which were first made in June by a man now 23.

"We took the allegation very seriously and took immediate action," Sesame Workshop said in a statement issued on Monday, US time. "We met with the accuser twice and had repeated communications with him. We met with Kevin, who denied the accusation."

The organisation described the relationship as personal and "unrelated to the workplace". Its investigation found the allegation of underage conduct to be unsubstantiated. But it said Clash exercised "poor judgment" and was disciplined for violating company policy regarding Internet usage. It offered no details.