In a statement posted on Facebook, the government said other countries should "not attempt to undermine (Libya's) authority".
Libya's air force bombed a Turkish vessel on Sunday after it entered Libyan waters and headed for the coastal jihadist stronghold of Derna, according to a lawmaker from the country's internationally recognised parliament.
"The Turkish boat tried to enter Libyan territorial waters by force... ignoring international norms and maritime regulations," the government said.
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Libya has had rival governments since August last year when an Islamist-backed militia alliance overran the capital, prompting its opponents to take refuge in the east.
The rival legislature in Tripoli issued a statement criticising "violent aggression" against the Turkish-owned ship.
The boat was "in international waters, 13 nautical miles off the coast of the town of Tobruk" in eastern Libya, Tripoli's foreign ministry said in a statement.
The UN mission in Libya also condemned the attack and called for a "thorough investigation" while urging "military actors in Libya... to undertake all necessary measures to avoid targeting civilians".