The home of Libya's disputed Prime Minister Abdul Hamid Dbeibeh was reportedly set on fire on Monday during protests triggered by reports that his Foreign Minister Najla Mangoush met her Israel counterpart Eli Cohen last week.
Mr Dbeibeh, who heads the Government of National Unity, suspended Ms Mangoush on Monday and ordered an investigation after Israel's Foreign Ministry claimed the two met in Italy.
As speculation mounted later on Monday that Ms Mangoush had been fired, and of her whereabouts, protestors blocked roads, burnt tyres and waved Palestinian flags in Tripoli and other western cities.
Mr Cohen said earlier he had spoken to Ms Mangoush about “the great potential for the two countries from their relations, as well as the importance of preserving the heritage of Libyan Jews, which includes renovating synagogues and Jewish cemeteries in the country”, Israel's Foreign Ministry cited him as saying on Sunday.
The meeting was reportedly organised by the Italy's Foreign Minister Antonio Tajani.
The announcement triggered protests across the country and gunfire was heard near the GNU's Ministry of Foreign Affairs in Tripoli.
In other cities, protesters gathered outside government buildings and blocked roads.
Initial reports claimed the UN's headquarters in Tripoli's densely populated Janzur district had been set on fire. However, an official close to the world body, speaking to The National, denied the claims.
Libya has never had any diplomatic ties with Israel.
The GNU's Foreign Ministry insisted that the meeting had been “unprepared and casual” but Libya's Presidential Council said it was not representative of Libyan foreign policy.
Council spokeswoman Najwa Wheba told The National that the meeting was in “breach of Libyan laws and legislations that criminalise dealing with the Israeli entity”.
“We had asked for an official clarification from the head of government to clarify how such a meeting was held and to take the subsequent steps according to laws and legislations,” she said.
A decision was subsequently taken to put Ms Mangoush in custody pending an investigation.
However, the minister has reportedly fled the country, with Ms Wheba saying she had “no knowledge” of her whereabouts.
Libya's Internal Security Agency denied claims it had allowed Ms Mangoush, who has a travel ban issued against her, to leave the country through Mitiga Airport.
Yair Lapid, leader of Israel’s opposition, criticised Mr Cohen for revealing details about the meeting.
“Countries of the world this morning are looking at the irresponsible leak of the meeting of the Israeli and Libyan foreign ministers and asking themselves: Is it possible to manage foreign relations with this country? Is it possible to trust this country?” he said.
However, diplomatic Israeli sources said Libyan officials had agreed to publicly announce details of the two-hour meeting, The Times of Israel reported.
On Monday afternoon Israel’s Foreign Ministry distanced itself from its earlier statement announcing the meeting.
"Contrary to reports, the leak about the meeting with the Libyan Foreign Minister did not come from the Foreign Ministry," it said.
Libya has a rich Jewish heritage, as is the case with other north African countries.
However, during the rule of Muammar Qaddafi, an estimated 38,000 Jews were expelled and most synagogues were destroyed and later turned into mosques.
Mr Qaddafi was a known antagonist of Israel and a champion for Palestinians, including armed militant groups.
After his removal and killing in 2011, Libya was plunged into a civil war that has left the country divided between rival governments in Benghazi, in the east, and Tripoli, in the west.
Mr Dbeibeh, who leads the government in Tripoli, is known for his close relations with Italy.
However, Ms Mangoush's meeting with Mr Cohen and what it entails could bring changes to domestic politics in Libya and a geopolitical shift in North Africa.