A Filipino construction worker has been killed in Libya allegedly for being a non-Muslim in the country's first beheading since 2011.

The murder, revealed in a statement from the Philippine Department of Foreign Affairs, is thought to have been conducted by a band of militia in Benghazi, though it is unclear which one.

The announcement comes at the same time as the Philippine government begins evacuating 13,000 of its citizens from the country, which is currently ravaged by armed conflict.

The government has put an Alert Level 4 in place in Libya - the highest alert to be instituted on countries in the midst of fighting.

The foreign affairs department claims that, as well as being Libya's first reported beheading in three years, the murder constitutes the first Filipino death in the Middle Eastern country since the start of the revolution in 2011.

The construction worker was kidnapped on 15 July at a checkpoint in the Gwarsha district of Benghazi. Libyan media sources report that the man's name was Antonio Espares, an employee of the construction firm Kibra.

A spokesperson from the department said the kidnappers demanded a random of $160,000. According to Philippine media, the construction company negotiated with the kidnappers for four days. The employee's remains were discovered at a hospital on Saturday.

The Filipino government has issued a statement urging all of its citizens in Libya to return home "as soon as possible" by contacting the Philippine Embassy in Tripoli to register for repatriation.