Field Marshal Haftar, who backs the House of Representatives government based in the eastern city of Tobruk, has long cultivated close relations with Moscow and relies heavily on Russian mercenary group Wagner for military support.
The Tobruk administration is a rival to the UN-backed Government of National Unity in Tripoli.
Field Marshal Haftar “held talks with Russian President Vladimir Putin and Defence Minister Sergei Shoigu”, his Libyan Arab Armed Forces group said on social media.
Kremlin spokesman Dmitry Peskov confirmed Field Marshal Haftar had held talks with Mr Putin.
“They discussed the situation in Libya and the region as a whole,” Mr Peskov said in comments reported by Russia's state news agency Tass.
It was the first meeting between the two men since 2019, according to Libyan media.
Field Marshal Haftar, who arrived in Moscow on Tuesday, had already held talks with Deputy Defence Minister Yunus-Bek Yevkurov there.
Mr Yevkurov has been a regular visitor to eastern Libya in recent years, most recently on September 17 when he met Field Marshal Haftar, days after floods devastated the coastal city of Derna, killing thousands of people and leaving thousands more missing.
A 2019 assault by Field Marshal Haftar's forces on the government in Tripoli relied heavily on Wagner mercenaries. However, it failed to overcome the Tripoli government's Turkish-backed armed forces.
After an October 2020 ceasefire brought the offensive to an end, Wagner redeployed some of its personnel, including to elsewhere in Africa – where Russia has long sought to boost its influence – and Ukraine, where the group took part in Moscow's invasion.
But despite repeated UN Security Council resolutions calling for the withdrawal of all foreign military forces from Libya, hundreds of Wagner personnel remain stationed in the east, as well as in areas of the desert south under Field Marshal Haftar's control.
Wagner's future plans are uncertain after leader Yevgeny Prigozhin was killed in a plane crash north-west of Moscow in August.