Libya's internationally recognised government has said it is suspending its participation in ceasefire negotiations hosted by the United Nations in Geneva, hours after an attack by renegade military commander Khalifa Haftar's forces on the capital's port.

In a statement late on Tuesday, the presidential council of the Tripoli-based Government of National Accord (GNA) said it would respond firmly to the attack at the appropriate time.

Earlier in the day, representatives of the GNA and Haftar's self-styled Libyan National Army (LNA), which launched a military offensive in April last year to seize Tripoli, had resumed indirect talks aimed at establishing a lasting ceasefire.

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Footage shared online showed thick black smoke rising from the port, a major gateway for food, fuel, wheat and other imports.

State oil firm National Oil Corporation (NOC) said it had urgently evacuated all fuel tankers from the facility after a missile struck metres away "from a highly explosive liquefied petroleum gas (LPG) tanker discharging in the port".

"Today's attack on Tripoli port could have led to a humanitarian and environmental disaster," NOC Chairman Mustafa Sanalla said.

"The city does not have operational fuel storage facilities ... the consequences will be immediate; hospitals, schools, power stations and other vital services will be disrupted," he said.

The attack happened as five military representatives from the GNA and another five from the LNA gathered in Geneva, more than a week after they ended their first round of negotiations without striking a deal that would help end the fighting in Tripoli.

In the previous round of talks, the UN mission said there was "broad consensus" between the two sides on "the urgency for Libyans to safeguard the sovereignty and territorial integrity" of the country, and to "stop the flow of non-Libyan fighters and send them out of the country".

Oil-rich Libya has been splintered between competing factions and militias since former leader Muammar Gaddafi was overthrown and killed during a NATO-supported uprising in 2011. It is currently split between two rival administrations - the Tripoli-based GNA and another allied with Haftar in the eastern city of Tobruk that controls key oil fields and export terminals. Each administration is backed by an array of foreign countries.

Earlier in the day Ghassan Salame, head of the UN Libya mission, had called the port attack a "big breach" of the fragile - and repeatedly violated - ceasefire that was brokered by Russia and Turkey on January 12 as part of efforts to de-escalate the battle for the capital.