Somalia security forces have killed 65 Shebab Islamic insurgents who attacked coastal towns in the semi-autonomous Puntland area in the country's northeast, the regional army chief said Monday.

"The fighting is almost over and the security forces are now pursuing the remnants of the militants" after five days of clashes, General Muhidin Ahmed Muse told reporters.

"Sixty-five of the militants who have been misled into this war, have been killed so far and 31 others, most of them children, were captured alive," he added.

The Al-Qaeda-affiliated Shebab was ousted from Mogadishu in 2011 and has since lost much of the territory it once held.

Shebab attacks have increased in tempo recently, seen as an attempt to destabilise the internationally-backed government ahead of an election due later this year.

A group of the Islamic insurgents stormed a Somali military base outside the capital Mogadishu early Monday, claiming to have inflicted heavy casualties.

Both the Somali authorities and the insurgents regularly report having inflicted significant losses on the other, claims that are often impossible to verify.

Government sources told AFP that military equipment was flown into Puntland last week to help the local security forces to battle the newly-arrived insurgents.

Several residents of the region said they saw Shebab fighters come ashore aboard fishing boats last week armed with machine guns, mortars and rocket launchers.

Around 100 insurgents sought to take control of the villages of Garmal and Suuj, near the port of Eyl, a pirate hotspot, local officials and residents said.

There has been no word from Shebab on the fighting or their reasons for their surprise deployment in Puntland.

Puntland set up its own government in 1998, but unlike neighbouring Somaliland, it has not declared full independence.