A group of One Show reporters performed the song on Let's Sing and Dance for Comic Relief on BBC One on Saturday.
But they didn't include a line about "gay, straight, or bi, lesbian, transgendered life".
A BBC statement said the song was shortened "purely for length". The band Iron Sun also sang the track - without that line - on the Let It Shine final.
The original song includes the line: "No matter gay, straight, or bi/lesbian, transgendered life/I'm on the right track baby/I was born to survive."
Other lyrics were also cut during the TV performances.
After Saturday's programme, the BBC said: "It is standard procedure to edit down music tracks to fit into the running time of the show."
But some viewers have complained on Twitter.
On Saturday, One Show reporters Angelica Bell, Dominic Littlewood, Michelle Ackerly, Iwan Thomas and Alex Thomas donned Lady Gaga-style outfits to perform the song.
And boy band Iron Sun sang a country-rock version of the track for Gary Barlow's TV talent show on 25 February.
The line "don't be a drag, just be a queen" was also cut.
After the the Let It Shine final, the show issued a statement to Gay Times saying "all the tracks were edited for length, musical beats and crucially to ensure the boys each had a section to showcase".
It continued: "Therefore, typically sections came out of all of the songs performed for the show.
"In this case, to get a dance break in, we did what we often do which was to repeat the first chorus as opposed to putting in the second one, especially as in this version of the song we had a slow version of the first chorus.
"It made sense therefore musically in an edit, to go with a repeated chorus with a faster tempo the second time around."
Follow us on Facebook, on Twitter @BBCNewsEnts, or on Instagram at bbcnewsents. If you have a story suggestion email entertainment.news@bbc.co.uk.
The BBC has defended cutting LGBT lyrics from two performances of Lady Gaga's Born This Way in the past month.