A top leader of Somalia's Al Shabaab rebels, intelligence chief Zakariya Ismail Ahmed Hersi, has surrendered to government and African Union forces and is now in custody.

Officials said he surrendered in the Gedo region, where Somalia borders Kenya and Ethiopia.

"Zakariya Ahmed was a very senior person who worked with [slain former Al Shabaab leader Ahmed Abdi] Godane," regional military official Jama Muse said.

"He was in charge of intelligence and finances, he was one of the senior Al Shabaab commanders who the Americans put a lot of money on their head."

The militant is the subject of a $3 million bounty as part of the US state department's Rewards for Justice program, which offers cash for information that helps disrupt terrorism plans.

Somali military official Mohamed Osmail said the militant had been hiding in a house in a border town and made contact with government officials to hand himself in.

Another intelligence source said the surrender was believed to have been motivated by a series of recent bloody splits and purges within the group, with Godane having ruthlessly eliminated many of his rivals, and his successor, Ahmad Umar Abu Ubaidah, continuing to maintain strict internal security.

Although presented by the officials as a senior Al Shabaab operative, it was unclear whether Zakariya Ahmed had still been active within Al Shabaab in recent months or weeks, or whether he was among a group of commanders who had already fallen out with Godane prior to his death.

There was no immediate comment from Al Shabaab.

AFP