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Libyan Interior Ministry Fawzi Abdul-Aal on Sunday resigned after scathing criticism about security forces' handling of an upsurge of violence in the country, reported local media.
Abdul-Aal's resignation was confirmed by Libya's state news agency, which gave no further details.
The resignation came shortly after an emergency meeting of the newly elected National Congress on security breakdowns in several areas of Libya.
The assembly accused the security agencies of being lax in responding to a recent series of violence in the country.
Two people were killed in the capital, Tripoli, in twin car bombings last week on the first day of the major Muslim Eid al-Fitr festival.
The authorities blamed the attacks on loyalists of Muammar Gaddafi's deposed regime.
Several shrines of Muslim saints were also destroyed in Tripoli and the western city of Zlitan in the past two days.
The attacks, blamed on hardline Salafist Islamists, were condemned by Mohammed al-Magariaf, the head of the National Congress.
“The congress will not hesitate to take firm decisions necessitated by the situation to track the perpetrators and bring them to justice,” he said in televised remarks late on Saturday.
Salafists, influenced by Saudi Arabia's Wahabism - a strict version of Islam - deem shrines idolatrous.
“The acts of some armed people in vandalising graves by force of arms and removing remains is not permitted by sharia (Islamic law) and is contrary to traditions,” the state authority responsible for issuing rulings on questions of Islamic law said, in a statement reported by the independent Solidarity Press news agency.
Libya Herald, an independent newspaper, reported that a Sufi Muslim shrine in Tripoli was partly demolished on Saturday.
Security forces protected the demolition operation, which was initiated by followers of a Salafist group, the report said.
A bulldozer was also used to destroy parts of the mausoleum of Sufi Muslim saint Al-Shaab Al-Dahman in the centre of Tripoli.
The North African country has seen several acts of violence, including deadly clashes among rival tribes and militias, since an armed revolt toppled Gaddafi last year.
A proliferation of weapons left over from the revolt against Gaddafi poses constant security threats. - Sapa-dpa