Van Gaal's squad has been ravaged by injury during this season but they have managed to win five straight games to sit third in the Premier League.
Phelan said Van Gaal's decision to change former fitness coach Tony Strudwick's role and alter the club's training were behind the injuries.
"What's happened is a continuation of the same players getting injured all the time, so you have to look to the reasons why," he told the International Business Times UK.
"I think Manchester United changed their thoughts on the fitness regime, they looked at it a little bit differently.
"Tony Strudwick, who was operating as head of sports science, was involved day to day with the first team. He understood the ins and outs of how to keep players fit, how to keep them ready for competition. Then suddenly they moved him sideways and did something completely different. That may have had an effect. That one area has changed.
"They've brought in new people with a different way of doing things. The intensity of training may be one thing - it may be too intense, or not intense enough - but obviously slight changes have been made with the present way of doing things.
"I would have thought [the squad] is big enough at Manchester United, because they can go out and get players in, but obviously they keep breaking down and they don't seem to be getting any better. They seem to get one back and lose another two."
Phelan backed former Netherlands coach Van Gaal to adapt and start learning what his players could handle.
The likes of Angel di Maria, Radamel Falcao, Michael Carrick and Phil Jones have spent time on the sidelines due to injury.
"He knows now roughly the intensity of the Premier League and what his players can produce," he said.
"He's been at the highest level, working with the highest players, in different countries.
"It's just a case of maybe understanding the specific requirements of players, individual players, where they need to be at certain times in order to perform. He's got enough staff there to sort that out."
