Freeman, who is hitting .417 with one homer and seven RBIs through the first five games, said team management did not tell him before making the decision.
"They didn't even give me a choice," Freeman said before Atlanta's game with the Chicago Cubs. "It's my career. I should be able to make that decision."
Freeman said he found out after arriving at Turner Field. He was examined by the team's medical staff on Saturday night after the Braves' 6-5 victory.
"They didn't even tell me anything," Freeman said. "I don't know what's going on. I'm pretty [angry] right now."
Braves general manager Frank Wren defended the move.
"Especially this early in the season, we're not going to take a chance to turn what would be two to three weeks into six or eight weeks by tearing that oblique area," Wren said.
Freeman said the injury first occurred in a workout March 31, the day before the season started, and that he wanted to keep playing through the pain. He winced and was favoring his right side while running to first on an RBI single in the eighth inning on Saturday.
Freeman will not travel with the team when Atlanta plays its next six games at Miami and Washington.
"It's not hurt to the point where I can't play," Freeman said. "I can play just fine. At least talk to me about it. You can't just make a decision without me knowing."
Blake DeWitt was called up from Triple-A Gwinnett to take Freeman's spot on the 25-man roster.
Wren said he wasn't upset that Freeman voiced his displeasure with the decision.
"He's a young guy that wants to play, and you appreciate that," Wren said. "You want him to be out there, but I think sometimes you have to protect players from themselves.
"This is not one of those situations where we want to lose him for the whole first half by letting him go out and tear that oblique area, and then we're dealing with a whole different injury," Wren added. "We think we've caught it early enough that he should be back in two to three weeks."