IS tried last week to seize export terminals in the so-called "oil crescent" of northern Libya, killing 56 people in two suicide bombings in Zliten and Ras Lanouf, east of Tripoli.
"On Sunday night, the guards intercepted three boats trying to enter the oil port of Zueitina," Ali al-Hassi, spokesman for the guards protecting oil facilities for Libya's recognised government.
"They opened fire and hit one of the boats. The other two made off but returned a short while later to tow the vessel which had been hit," he said.
IS has been trying for several weeks to push east from its coastal stronghold of Sirte, threatening to seize control of Libya's oil wealth.
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Libya descended into chaos following the 2011 ouster and killing of longtime dictator Moamer Kadhafi.
It has had rival administrations since August 2014, when an Islamist-backed militia alliance overran Tripoli, forcing the government to take refuge in the east.
The United Nations is pressing both sides to accept a power-sharing agreement it hopes will help to reverse IS's territorial gains.
It had a pre-revolt output capacity of about 1.6 million barrels per day, but unrest has forced a major slump in production, and output now stands at around 500,000 bpd.