Somalia's Al-Qaeda-linked Shebab militants stormed an African Union base Friday, the Somali army said, with witnesses reporting several dead.

"They launched an offensive on a military base at El-Adde and there was heavy fighting which caused casualties,"  Somali army colonel Idris Ahmed said, adding a Shebab suicide commando blasted a way into the base in the far southwestern Gedo region, which borders Kenya and Ethiopia.

Both Somali troops and Kenyan soldiers with the AU force, AMISOM, are deployed at that base.

"There was suicide attack followed by the fighting and it seems that the base was stormed," Ahmed said.

Shebab spokesman Shebab spokesman Abdiaziz Abu Musab claimed to have killed 63 Kenyan troops in the pre-dawn attack, but this could not be immediately verified.

"The mujahedeen fighters carried out a successful operation this morning on a military base at El-Adde, and they have killed many of the Christian soldiers from Kenya," Musab said.  "We have counted 63 dead bodies inside the base."

The Shebab frequently exaggerates the number of troops they kill, while AMISOM rarely gives exact tolls.

Kenya's army said Friday morning fighting was ongoing, and insisted that it was the Somali army base next door to its camp that was seized.

"Al-Shebab militia attacked... the KDF troops under AMISOM counterattacked, the fighting is still going on," said Kenya army spokesman David Obonyo.

Local elder Hussein Adam said he heard a huge explosion followed by intense gunfire for about 45 minutes, and that the Shebab had overrun the base.

"We don't know about the casualties, but people who went there saw many dead bodies strewn around," he said, having spoken to those who went to the base.

The Shebab, fighting to overthrow Somalia's internationally-backed and AU-protected government, has launched a string of similar attacks.

In September 2015, Shebab fighters stormed a Ugandan AMISOM base in Janale district, 80 kilometres (50 miles) southwest of Mogadishu in the Lower Shabelle region.

And in June, Shebab killed dozens of Burundian soldiers when they overran an AMISOM outpost northwest of Mogadishu.

The militants also stage frequent suicide attacks in the capital.

But the 22,000-strong AMISOM force has also made significant gains against the Shebab, pushing them out of several strongholds in the southwest of the country.