"I'm seeing the discussion around Afro-Latino representation in our film this weekend and it is clear that many in our dark-skinned Afro-Latino community don't feel sufficiently represented within it, particular among the leading roles.
"I can hear the hurt and frustration over colourism, of feeling still unseen in the feedback.
"I hear that without sufficient dark-skinned Afro-Latino representation, the work feels extractive of the community we wanted so much to represent with pride and joy."
Lin-Manuel said the team "fell short" of their goals, and thanked people for "raising" their concerns.
He continued: "In trying to paint a mosaic of this community, we fell short. I'm truly sorry.
"I'm learning from the feedback, I thank you for raising it, and I'm listening."
The star - who plays Piragüero in the movie as well as serving as producer, having written the music for the original Broadway show - noted he is still very proud of the film, although he acknowledges the need to "be accountable for our shortcomings".
He added: "I'm trying to hold space for both the incredible pride in the movie we made and be accountable for our shortcomings.
"Thanks for your honest feedback. I promise to do better in my future projects, and I'm dedicated to the learning and evolving we all have to do to make sure we are honouring our diverse and vibrant community."
