The attack began with a blast at the remote Af-Urur camp, about 100km west of the commercial hub of Bossaso, before the fighters overran the base and killed soldiers at close range, said Ahmed Mohamed, a senior military official.
Close to 70 people were killed, though an exact death toll was not yet available, Mohamed said.
Abdi Hersi Ali, Puntland’s interior minister, said troops suffered casualties but he declined to give further details.
Officials called it the region’s deadliest attack in years, highlighting the dual challenges facing security forces from the al-Qaeda-linked al-Shabab and the growing presence of fighters linked to the Islamic State of Iraq and the Levant (ISIL) group.
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“The situation is grim over there. This attack was an unexpected one,” Mohamed said.
The armed fighters, including suicide bombers, reportedly attacked the base from three directions, forcing soldiers to retreat.
Colonel Hashi Ahmed, a senior military official, told the Associated Press news agency that reinforcement troops reached the area and drove the fighters out of the camp. He estimated that at least 100 fighters were involved in the attack.
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Al-Shabab claimed to have killed at least 61 soldiers. They also seized a large amount of weapons and ammunition and more than a dozen military vehicles in the assault.
Puntland in northern Somalia also faces a growing threat from ISIL-linked fighters who have split from al-Shabab.
The assault came days after Puntland sentenced to death five al-Shabab members who were arrested as they drove a vehicle carrying three barrels packed with explosives into Bosaso, Puntland’s capital, on April 26.
Al-Shabab, which is fighting to overthrow the internationally recognised Somali government, has launched a series of deadly incursions in neighbouring Kenya, which has contributed troops to the Somalia-based African Union peacekeeping force.
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