Former Libyan prime minister Ali Zeidan has fled to Europe after parliament voted him out of office on Tuesday over his failure to stop rebels exporting oil independently in a brazen challenge to the nation's fragile unity.

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.