Shanahan said he learned of the injury as practice came to a close and that James may need surgery.
"He just got an MRI and we just found that out," Shanahan said.
Shanahan added later in his post-practice media session that James' injury was not ACL-related.
"It started bothering him yesterday in practice so we shut him down halfway through practice, and I think he got the MRI this morning," Shanahan said. "(The name of the injury) started with an M. And I know six weeks. They said around six weeks, so I'm guessing."
James' injury is a notable development at the wide receiver position for the 49ers given the uncertainty over which players will wind up making the 53-man roster. James is among a group competing for spots behind Deebo Samuel and Brandon Aiyuk that includes James, Jalen Hurd, Travis Benjamin, Mohamed Sanu, Trent Sherfield, Jauan Jennings, and Nsimba Webster.
The injury also changes the picture a bit in terms of the return specialist position. James has been one of the 49ers' primary return specialists over the course of his career, but the 49ers may need to turn to a player like Travis Benjamin or Nsimba Webster to fill that role.
Shanahan was asked Friday if he's seen enough from Benjamin or Webster to be confident in either of them in the return game.
"I think with us, I think it's really hard to make a team as the returner," Shanahan said. "You have to be one of those six (receivers). If you're close to one of those guys, the fifth or sixth guy -- usually it's got to be the fifth guy because you only get five guys up on game day -- if you're close to that guy and you have return skills or you're a gunner or you bring something else to the table, then you can pass a guy who might be a little bit ahead of you as a wideout. But if you're not close to being able to contribute as a wideout, it's really tough to make it as a returner. I think both of those guys -- Travis and Nsimba -- have done some really good things for us. They went in at receiver and we know they have some experience in their careers as returners too."
James, 25, is in his fourth season with the 49ers after being selected in Round 7 of the 2018 NFL Draft out of Middle Tennessee. James had career highs in receptions (23) and receiving yards (394) in 2020 and has 38 career receptions for 689 yards and three touchdowns. He has 47 career kick returns for 1,081 yards (25.2 average) and one touchdown along with 51 punt returns for 373 yards (7.3 average).
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