Harris' latest musical comedy -- about a transgender punk rocker -- is open for improvisation and audience interaction, and according to his rep, the 40-year-old actor was in character when he told a member of the audience: "I'm doing something up here, mother [expletive]."
"The response to the fan yelling was actually done in character -- Neil as Hedwig, not as though Neil stopped the show to respond out of character," said the rep.
"When the fan initially yelled, 'I love you, Neil,' Neil (as Hedwig) then responded, 'Who's Neil? I'm not Neil.' He then looked over at Yitzhak (played by Lena Hall) and said, 'Are you Neil? You better not be Neil' followed by Hedwig then offering the quote in question."
"It was all done in good fun, and fully in the context of the show," he continued. "The audience went crazy and it really was a light-hearted moment, which is not being properly contextualized in any of these various posts."
Harris himself addressed the issue via twitter on Sunday, asking fans to get the "full story/context" before making judgements.
2014: The Year in Music [PHOTOS]