In a late-Sunday tweet, the video-sharing website said, "LGBTQ+ videos are available in restricted mode, but videos that discuss more sensitive issues may not be."
The company declined to elaborate on what is classified as sensitive.
The response came after several popular YouTube stars took to social media over the weekend to complain about the restricted mode, which the company says is meant to protect children and families.
"We are so proud to represent LGBTQ+ voices on our platform," the YouTube statement said. "They're a key part of what YouTube is all about."
YouTube, a subsidiary of Google, said it regretted the confusion that the mode has caused, adding that is looking into the concerns. The restricted mode is an optional feature that users have to turn on.
YouTube has acknowledged that the restricted mode — which it says uses community flagging, age restrictions and other means to identify and filter possibly inappropriate content — is "not 100 percent accurate."
The criticism came after multiple YouTube creators said their content on topics such as same-sex relationships and coming out were hidden by default in the restricted mode.
Rowan Ellis, one of the first video bloggers to voice concern over the mode, said the issue made her "really, really angry."
"This is something that no one's really sure of how it's working, but we know that it has some type of targeted effect on LGBT individuals," Ellis said in a YouTube video posted Thursday. "I think it's really important to look at why LGBT content has been deemed as inappropriate."
Other social media users used the hashtag YouTubeIsOverParty to voice their concerns about the censoring issue.
One of YouTube's biggest stars, Tyler Oakley, who has more than 8 million subscribers, said his recent video "8 Black LGBTQ+ Trailblazers Who Inspire Me" was restricted, even though he says it did not feature adult content.
Oakley, who was listed by Forbes as one of YouTube's highest-paid creators last year, has become known for his activism in the LGBT community.
"Still not fixed," Oakley tweeted late Sunday. "One of my recent videos '8 Black LGBTQ+ Trailblazers Who Inspire Me' is blocked because of this. I'm perplexed."
He urged YouTube users to "actively check on all LGBTQ+ creators you're subscribed to & continue to support their content."