Froome's Team Sky colleague Tiernan-Locke faces action over a doping violation following analysis of his biological passport.
Tour de France winner Froome believes it is inevitable his own reputation will be damaged as a result.
"Definitely. Inevitably that's the reality of it," Froome told the BBC.
"It's hugely unfortunate for the team this is now happening."
Tiernan-Locke, 28, denies any claims made against him and will not ride again until disciplinary proceedings come to a close. He was forced to pull out of the 2013 World Championships after being asked to explain recent biological passport results.
Team Sky were quick to state that the tests were conducted before they had signed him from Endura and will now await the results of a hearing before deciding whether he will ride for them again.
"It's still being contested and there's going to be a trial," added Froome. "I think we're going to have to wait until the end of the trial to actually know exactly what's going to happen."