Confirmation of a French military presence in Libya caused outrage in the restive country. Hundreds of Islamist supporters and the UN-backed unity government accused Paris of backing a powerful militia commander who challenges both groups.

The anger in Libya sparked after it was revealed that Paris is helping the troops of Khalifa Haftar, a powerful military commander challenging the Libyan government.

The military cooperation was exposed to the public by the deaths of three French Special Forces troops, who died in a helicopter crash along with several Haftar men near Benghazi, when the aircraft was allegedly shot down by a militia group opposing the commander.

The Government of National Accord (GNA) condemned the French intervention in a statement released on Wednesday evening, demanding explanation from Paris and saying that it would not compromise on Libyan sovereignty.

"The Presidential Council expresses its deep discontent at the French presence in eastern Libya without coordination with the Council, which was declared by the government of France," said the statement from the unity government.

The statement posted on the government’s Facebook page said that “nothing justifies an intervention without our knowledge and without coordinating with us.”

Hundreds of Libyans in several cities, especially capital Tripoli and Misrata, marched in a protest against the French intervention, Libyan TV channels shown on Thursday. The protests were fueled by several prominent clerics, who denounced Western intervention in Libya and GNA.

"Get your hands off Libya," read placards held by protests in the capital. "No French intervention," read another.

The demonstrators burned a French flag.

The Benghazi Defense Brigades, the militant group that claimed responsibility for the downing of the helicopter, said 13 of its fighters were killed in what it described as French retaliation airstrikes in western Benghazi. France denied that its warplanes over Libya were used for any missions but reconnaissance.

Providing military support to Haftar, puts France in a legally-dubious position, as the commander does not have an official capacity in the UN-recognized government and is in no position to seek military aid from foreign powers.

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Paris however is far from the only Western nation to conduct clandestine operations in Libya, evidence indicates. Last month records of what appears to be communication between Haftar troops and British, French, Italian and US forces coordinating airstrikes against various armed groups opposing the general were leaked online.

The problem with such clandestine interventions is that they often disregard the law and have no public oversight, Stop the War Coalition’s Chris Nineham told RT.

“They are not backed by the UN, these interventions. They are not checked anywhere. They are just unilateral acts of military aggression,” he said.

Haftar is a former general under Muammar Gaddafi, who was disavowed by the Libyan strongman in the late 1980s during Libya’s war with Chad, when the military commander was captured. He was allowed into the US and lived there until 2011, when he returned to Libya and sided with the West-backed rebels during the 2011 uprising against Gaddafi.

While Libya was effectively split between an Islamist alliance in the capital and a UN-backed government in eastern Tobruk, Haftar was appointed chief of the Libyan Army and led a large operation against the Islamists. But when the UN-backed unity government was formed in Tripoli in December 2015, he refused to support it and keeps his powerbase in the east.

The country remains split, with the eastern part issuing its own currency, conducting oil trade and otherwise keeps acts independently from the capital. The fractured nature of Libya allowed Islamic State (IS, formerly ISIS) to secure a foothold in Sirte, Gaddafi’s home city, which was turned from a power center into a site of political irrelevance after the leader’s demise.

France played a key part in the NATO operation, which turned the tide for the rebels in 2011 and resulted in Gaddafi’s summary execution and de facto dissolution of the once-prosperous country into warring states.