The self-declared government in Tripoli and some armed factions in the city oppose the unity government and have warned it not to move.
The Tripoli government was brought to power after armed brigades backing it won a battle for the capital in 2014. A rival government moved to eastern Libya.
The unity government is the result of a December deal to heal Libya`s divisions and end its armed conflict, but the new government has faced opposition from hardliners in both the east and west of the country.
On Sunday and Monday Tripoli`s airspace was closed for periods of several hours, a move that the unity government`s Presidential Council said was designed to prevent it traveling into Libya.
Tripoli Prime Minister Khalifa Ghwell said in a statement late on Tuesday that the airspace had been closed to "protect the souls of the people following the Presidential Council`s inappropriate behavior".
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