Dendias was about to be welcomed by his Tripoli counterpart, which Athens says was not agreed on.
Greece’s foreign minister called off the first leg of his visit to Libya just moments after landing in Tripoli on Thursday.
Nikos Dendias was on a two-part trip to meet Libya’s rival western administration in the capital and the east-based administration in the city of Benghazi.
But he refused to disembark from his plane in Tripoli when his counterpart, Najla Mangoush, came to the airport to greet him. Instead, Dendias flew to Benghazi ahead of schedule.
Mangoush signed the controversial Turkish-Libyan oil and gas exploration deal in October -- a move Athens blasted, claiming the Tripoli government was not authorised to do so.
Dendias earlier requested to be greeted by the president of Libya’s National Transitional Council, Mohamed Younis Menfi, and that no one else would be present for the meeting, the Greek press reported.
The Greek Foreign Ministry described the incident as a violation of protocol and the agreed terms for the visit.
In a terse statement, Athens condemned the move and promised to retaliate "with appropriate diplomatic measures".
Gas deal fuels further Mediterranean feuds
Since March, two governments have been battling for power in Libya after the 2011 uprising.
A spokesperson for the Tripoli-based government said Mangoush’s presence at the airport was part of diplomatic conventions and that Dendias had left the city "without offering explanations".
In response, Tripoli said it had recalled the Libyan ambassador in Athens and had summoned the Greek chargé d'affaires.
Tensions have been rising in the Mediterranean following a controversial maritime and gas deal between Turkey and the Tripoli government.
Last month's preliminary deal has been rejected by both Greece and Egypt, who also accuse Turkey of using the agreement to try to expand its influence in the region.
During a Cairo visit last month, Dendias said the deal infringes on Greek maritime borders.
In 2019, Turkey signed another controversial maritime border deal with Tripoli, granting it access to a contested economic zone in the eastern Mediterranean.
The deal ignored the existence of several Greek islands, including Crete, and reignited tensions over oil and gas drilling rights.
Meanwhile, Cairo and Athens have strengthened ties in recent years, including signing new maritime border agreements with Cyprus.