The pupil, at Gleed boys' school in Spalding, was found to have set up a page on the popular networking site Bebo, inviting classmates to "kill" a young female member of staff and encouraging them to post abusive comments.
A source close to the school said: "This boy has had incidents with other staff before and in this case there was a clash of personalities."
The headteacher permanently excluded the boy at Easter, but the decision was overruled by the governors, The TES has been told.
Staff are thought to be unhappy about the U-turn and an official ballot, planned for this month, may lead to them refusing to teach the boy.
Ken Rustard, the regional secretary for the National Union of Teachers, said: "This incident is completely unacceptable."
Geoff Cowley, the headteacher, said: "I made a decision, which I felt was correct at the time, but the governors made theirs and I respect that. I am obliged to ensure he is reintegrated into the school."
The teacher in question is now off sick due to stress.
A study by the Teacher Support Network earlier this year found one in five staff had been the victim of cyber-bullying, with pupils topping the list of perpetrators. They were responsible for a third of incidents; 17 per cent took sick leave as a result.
Chris Keates, the general secretary of the NASUWT, said: "We receive many calls from teachers who are dissatisfied with the way their school reacts to these incidents. All schools should have a cyber-bullying policy."