Zeidan was in Malta for two hours late on Tuesday on a short stop before going to “another European country”, Prime Minister Joseph Muscat told state-owned television TVM.
Government sources in Malta said he had left via a private plane bound for Germany, but the German authorities could not confirm he had arrived.
The standoff over control of oil exports runs across dangerous regional and tribal faultlines in Libya where rival militias with powerbases in the east and west back competing political factions in the transitional government.
Western powers, who supported the NATO campaign that came to the aid of the anti-Gaddafi rebellion, fear the OPEC member state could slide into greater instability or even break apart, with rival groups laying claim to power and vast oil reserves.
Parliament acted after rebels holding three key ports in the east disobeyed government orders and loaded a North Korean-flagged tanker with oil at Es Sider port as part of their drive for a federal state in their eastern region.
Although Zeidan had threatened to use force to stop the vessel leaving, the tanker managed to reach international waters and flee, undermining the prime minister’s credibility.
Malta’s Muscat said he spoke briefly to Zeidan, who lived for many years in Europe before the 2011 uprising encouraged exiles like him to return to a North African country still struggling to shake off four decades of Gaddafi’s one-man rule.
Libya’s state prosecutor Abdel-Qader Radwan had issued a travel ban on Zeidan because he faces an investigation over alleged irregularities involving misuse of state funds.
The General National Congress (GNC), Libya’s transitional assembly, named Defence Minister Abdallah al-Thinni acting prime minister for two weeks. Deputies plan to pick another replacement in the interim ahead of a parliamentary vote expected later this year.
Whoever is chosen will face a mammoth task trying to unite and cajole a country deeply divided along tribal, regional and political lines, where hardline Islamists oppose more liberal leaders such as Zeidan.
“We are new to this political game. We are still learning,” said Salah Elbakhoush, a Tripoli-based political analyst.
“But we hope that there will be an improvement after Zeidan left,” he said.
NO ARMY, NO CREDIBILITY
Libya has lurched from crisis to crisis since the fall of Gaddafi nearly three years ago, and many Libyans are frustrated by the slow progress in their transition to democracy.
The country still has no effective army or police, and the government is in danger of running out of money because the rebel activity at oilfields and ports have dried up vital oil revenue. Oil output has fallen to a trickle.
That has left powerful groups of former rebels and militiamen to often step into the vacuum in a country still awash with arms from Gaddafi’s days and the revolt that ended his rule.
The Misratan militia, based in the port town of Misrata and loosely allied with Islamist parties in the GNC, has already been gathering forces to support the government and face off with fighters loyal to the eastern federalists who seized the ports.
But analysts said their main rivals, the Zintanis in the mountain town of Zintan near the northwest border with Tunisia, are unlikely to want the Misratans take a larger role in the country’s security without reacting themselves.
How far those rivalries will erupt is unclear, with alliances often shifting in the complex network of interlacing disputes. Clashes broke out on Tuesday between rebel gunmen and pro-government forces in Sirte, a central coastal city dividing western and eastern Libya.
“With control of the central government and Libya’s oil at stake, all of these groups, rivalries, and alliances of convenience are coming to the fore,” said Geoff Porter, North Africa specialist at West Point’s Combating Terrorism Center.
“One of the reasons that Libya has reached this impasse is that dialogue had failed, not least because there was no one in Libya that could speak authoritatively and had the capacity to translate words into action.”
There was no still word on the whereabouts of the tanker which sparked the crisis that led to Zeidan’s ouster.
A military spokesman said on Tuesday that Libyan gunboats chased the tanker along Libya’s eastern Mediterranean coast and opened fire, damaging it, and said Italian naval ships were helping move the tanker to a Libyan government-controlled port.
But Italy denied any of its vessels were in the area at the time and the reported incident of a naval ship opening fire could not be confirmed. The navy and defence ministry have not been available for comment since.
The eastern rebels are made up of former oil security forces who defected with their leader Ibrahim Jathran, a former Gaddafi fighter, in the summer and took over the oil terminals to claim more autonomy for their self-declared Cyrenaica region.
Zeidan’s government tried for months to mediate an end to the ports seizure, and Cyrenaica leaders had claimed an agreement was close.
Support had seemed to be waning for Jathran after the six-month ports closure, and the navy had already opened fire on a Maltese-flagged tanker trying to approach Es Sider in January.