Mr Zeidan was in Malta for two hours late on Tuesday on a refuelling stop before going to "another European country", Maltese Prime Minister Joseph Muscat said.
The stand-off over control of oil exports threatens to deepen dangerous regional and tribal faultlines in Libya where rival militias with powerbases in the east and west back competing political factions in the transitional government.
Western powers fear the Opec member state could slide into greater instability or even break apart.
Parliament acted after rebels holding three key ports in the east disobeyed government orders and loaded a North Korean-flagged tanker with oil as part of their drive for autonomy.
Mr Zeidan threatened to use force to stop the vessel leaving but it reached international waters.