"Any military action must be done with the cooperation of the Libyan authorities," government spokesman Hatem el-Ouraybi told AFP by telephone.
"The military option to deal with the boats inside Libyan waters or outside is not considered humane."
Brussels gave the green light to a mission that would see warships and reconnaissance aircraft deployed in the Mediterranean after a series of deadly shipwrecks in which hundreds of people have drowned trying to reach Europe.
"The government will not accept any violation of Libyan sovereignty," Ouraybi said, and "will not accept the plan unless it is coordinated" with Libya's internationally recognised administration.
The EU is still waiting for a UN resolution that will allow it to destroy boats belonging to people smugglers in Libyan waters, the epicentre of the humanitarian disaster unfolding on Europe's southern shores.
Libya has descended into chaos since the NATO-backed ouster in 2011 of longtime dictator Moamer Kadhafi, with rival governments and powerful militias battling for influence in the oil-rich North African state.