Students have been told they may return to the Science Center, the last of four buildings to be cleared. The final clearance was issued Monday afternoon through Harvard's emergency alert system.
The FBI was investigating, along with Cambridge and university police and other agencies.
Harvard officials would not say how they received the report and would not comment on speculation among students that it could have been a hoax timed to coincide with finals week at the Ivy League school.
Students were first informed of the report shortly after 9 a.m., just as some finals were about to get underway.