Wednesday's decision ends an encampment dating to October, but the group still plans a presence at a site across the street in downtown Cleveland.
A spokeswoman for Mayor Frank Jackson promised a comment later Wednesday.
Occupy Cleveland media contact Joseph Zitt says five men charged in the bomb plot had done work for the group but says Occupy Cleveland is a nonviolent group with no knowledge of any bomb plan.
Zitt says the group won't speculate on the timing of the permit denial. He says the group was surprised but is acknowledging the city's right not to renew the permit.