"It's a really good sequence and it will probably end up on the DVD so people can see it. But like many things in the editing process, it was an embarrassment of riches and it was just one of the things that had to go," he said.
"Unfortunately, it was the one and only sequence Anna Paquin was in, the Rogue character was in. Even though she's in the materials and part of the process of making the film, she won't appear in it."
However, Singer was quick to emphasise the decision to cut the True Blood star's screen-time had nothing to do with her performance.
"She did a fantastic job," Singer said. "She was awesome in the sequence. She's a brilliant actress. I would work with her in a heartbeat."
He said Paquin "completely understood" his decision.
"It's very disappointing, but she's very professional and she knows that stuff happens, particularly with material you shoot early on in production. Films evolve," Singer said.
The film, which is scheduled for release next May, features a slew of A-list stars including Hugh Jackman, Jennifer Lawrence, Halle Berry and Michael Fassbender.
Paquin won the Oscar for best supporting actress for her role in The Piano - her first acting role - in 1994 aged just 11.