The song Heated, which was released on Friday, contained a derogatory term that has often been used to demean people with spastic cerebral palsy.
It “will be replaced in the lyrics”, they added, without giving a timescale.
The backlash came just a couple of weeks after US pop star Lizzo apologised for using the same word in her song GRRRLS.
Within days, she apologised and re-released the song, omitting the offensive lyric.
“Let me make one thing clear: I never want to promote derogatory language,” she wrote in a statement posted to social media.
“As a fat black woman in America, I've had many hurtful words used against me so I understand the power words can have (whether intentionally or in my case, unintentionally).”
“I'm tired and frustrated that we're having this conversation again so soon after we got such a meaningful and progressive response from Lizzo”.
Disability charity Scope also asked Beyoncé to re-record the song, omitting the insult.
“Words matter because they reinforce the negative attitudes disabled people face every day,” said media manager Warren Kirwan.
“Beyoncé has long been a champion of inclusivity and equality, so we'd urge her to remove this offensive lyric.”
Other fans defended the star, pointing out that the term can have a different meaning in the US – where it is often used to mean “freaking out” or “going crazy” (although those terms can themselves be insensitive to people with mental health conditions).
Despite the controversy, Beyoncé's seventh studio album, Renaissance, is expected to top the charts around the world this week.
In the UK, it is currently outselling the rest of the top five combined.
The lead single, Break My Soul, is also expected to top the charts.