The separatists are former rebels who have turned against the interim authorities in the restive North African country after toppling veteran dictator Moamer Kadhafi in the 2011 uprising.
Separatists have been blockading oil terminals in eastern Libya that they had been entrusted with guarding over demands for autonomy in eastern regions and a share in lucrative oil revenues.
Yesterday, they began loading oil onto the Panamanian-flagged "Morning Glory" tanker docked at Al-Sidra terminal.
Today, Culture Minister Amin al-Habib said Libyan navy ships had been deployed at sea to stop the tanker from leaving port.
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"The tanker cannot leave any more, or it will be turned into a pile of metal," he said at a press conference.
The defence ministry also said orders for military action had been issued to the armed forces, the official Lana news agency reported.
The ministry ordered the chief of staff, the navy and the air force "to deal with the tanker that entered Libyan waters without a prior permit from the legitimate authorities," Lana said.
Harairi said he expected the operation to continue until the end of today, noting that the ship could take up to 350,000 barrels of crude oil.