Lebanese troops claim to have overrun the compound of a firebrand salafist cleric whose followers had killed at least 16 soldiers during two days of running battles near the southern city of Sidon.

The army death toll is the worst in the past six years and has amplified already heightened sectarian tensions in Lebanon, which is struggling to contain a spillover from the Syrian civil war.

The whereabouts of the cleric, Ahmed Assir, a vehement anti-Hezbollah figure, remained unknown late on Monday. However, most of his followers had either been captured or killed, the army said. Assir had earlier vowed to fight to the death.

By nightfall, sporadic gunfire was reported in renowned flashpoint areas across Lebanon and political leaders called for a curfew in the capital Beirut, as well as Tripoli and Sidon. Tyres were burned on main roads in the north of the country and checkpoints briefly set up by masked men.

Leaders of all sects urged calm throughout the early evening and some later expressed confidence that the flare-ups were acts of defiance, rather than signs of a profound decay in security.

The battle in Sidon marks the first time the Lebanese military has been directly drawn into a major clash since the Syrian uprising began in March 2011. It claimed its hand was forced after three soldiers were killed by gunmen linked to Assir at a checkpoint east of Sidon early on Sunday. The death toll rapidly escalated on both sides, with up to 20 gunmen also thought to have been killed in several days of fierce fighting.

The Lebanese army has attempted to maintain a neutral stance as sectarian tensions have mounted in the past two years. However, it has been accused by Assir and some Sunni political figures of giving cover to Hezbollah, particularly during the Shia Islamic militia's large-scale operation in Syria over the past month.

Assir had accused Hezbollah's leader, Hassan Nasrallah, of fuelling a sectarian war in Syria by sending large numbers of his fighters late last month to overrun the Sunni town of Qusair on the Lebanese-Syrian border.

Both sects have been polarised by the neighbouring crisis, which has pitted largely Sunni supporters of the opposition against Shia supporters of the Assad regime, and inexorably drawn them into a broader regional standoff.

Critics of Hezbollah in the Sunni Arab world have vowed to level a series of punitive measures at the group and those they allege to back them. Gulf states, among them the UAE and Qatar have said they are considering expelling Lebanese citizens who they claim are linked to the organisation. However, the warning is being perceived in Lebanon as potentially a collective punishment, which could jeopardise the estimated $8bn in remittances sent back annually from the Gulf Co-operation Council (GCC) states by Lebanese expatriates.

Some GCC leaders have said they will draw no distinction between sects in deciding who to punish and have emphasised that Hezbollah's political bloc controls the Lebanese government, with the support of a large Christian bloc led by a retired general, Michel Aoun.

Sunni leaders on Monday joined leaders of rival sects in expressing their support for the Lebanese military, which despite its fraught position is still regarded by many as the fragile state's only binding institution.

A statement from the army command vowed to "suppress sedition" and claimed that the fighting in Sidon had been suppressed.

Beirut, which is already suffering the effects of a tourism and economic downturn caused by the crisis in Syria, remained largely quiet on Monday night, with many businesses shuttered and many streets eerily empty.