Holland, 32, said the Giants placed him on the injured list earlier this season with a non-existent finger bone bruise on his left index finger.
"I'm not happy about that, but at the end of the day, I'm going to do whatever they ask me to do," Holland told the San Francisco Chronicle.
Holland was demoted from the starting rotation to the bullpen this weekend. The veteran pitcher added he has "no idea" what the front office is doing.
Giants president of baseball operations Farhan Zaidi denied Holland's claims. Zaidi told the San Francisco Chronicle the finger injury was legit and the team has "extensive medical records" of it.
"His use of the word 'fake' probably comes from him feeling he could continue to pitch with it," Zaidi said. "Players and the staff and front office people sometimes have differences of opinion when they should or shouldn't play."
Tyler Beede replaced Holland in the starting rotation. Holland is 1-4 with a 6.75 ERA this season.