The source added that it is unclear if it's an old or new injury.
The source said Boller plans to hold off surgery for now and plans to try treatments for a week or more in hopes that the shoulder will improve; if it does not, he will then have surgery.
Ravens general manager Ozzie Newsome told reporters Wednesday that while Boller is facing a serious shoulder injury, he does not need surgery at this time.
"Kyle Boller could play again this season," Newsome said. "That could change, but this is good news."
The Ravens said they are waiting until Friday for the results of tests Boller has this week to determine his status for the season.
The Carroll County (Md.) Times first reported Wednesday that initial results of an MRI on Boller's injured throwing shoulder were not favorable -- and that the team was awaiting a second opinion.
Boller was unable to throw Tuesday and has struggled to raise his right arm over his head, the newspaper reported. While jogging onto the field, he never moved his right arm and crossed his left arm across his body to scratch his right ear, according to the newspaper.
"We'll see how it goes day to day," Ravens coach John Harbaugh said of Boller, who was injured in the Ravens' preseason game against the Minnesota Vikings. "He's got MRIs that are being looked at."
With quarterback Troy Smith battling a viral illness, and top draft pick Joe Flacco the only healthy option heading into Thursday night's preseason finale with the Falcons, the team has signed free agent QB Casey Bramlet.
Boller's injury, along with Smith's continued recovery, might force the Ravens to play rookie Flacco for all of Thursday's preseason finale against the Atlanta Falcons -- and possibly hand Flacco the starting job by default.
Smith attended team meetings Tuesday morning but didn't have the energy to stay beyond that, Harbaugh said, according to The Baltimore Sun. He is dealing with dehydration after not eating for four days and is expected to be a game-time decision for Thursday's game.
"We'll know before the game, but it could go up to the game," Harbaugh said of Smith, according to The Sun. "It just depends on how fast he gets his strength back. You would love to be able to predict it and say, 'Hey, we know what's going to happen,' but there's just no way to know. We want him to play and he wants to play."
ESPN's Chris Mortensen contributed to this report.