The Twitter posts mentioned Michigan's open carry law for firearms as well as "calling the morgue." Harbaugh's Twitter handle was tagged in the string of posts.
The tweets, which authorities said came from an account claiming to be a player once associated with Harbaugh's Michigan team, have since been deleted.
A Michigan confirmed that the player whose Twitter account was the source of the threats left the program last November.
University police officers were watching the Michigan football training facility, according to sources within the program, and the Ann Arbor Police Department had been notified of the threats.
"Safety is always our No. 1 priority," said Melissa Overton, university police deputy chief and spokeswoman. "I can't go into any details about it, but that is our No. 1 priority."
Overton said she could not say more because the investigation is ongoing.