Somalia will expel thousands of Ethiopian troops stationed in the country to help with security by the end of the year unless Addis Ababa scraps a disputed port deal with the breakaway region of Somaliland, a senior Somali official said on Monday.

Security experts and foreign diplomats said the move risks further destabilising Somalia as local forces would be unable to fill the security vacuum, which would likely be exploited by fighters from al Shabaab, an affiliate of al Qaeda.

At least 3 000 Ethiopian soldiers are stationed in the Horn of Africa country as part of an African Union peacekeeping mission (ATMIS) fighting al Shabaab, which controls large portions of Somalia, while an estimated 5 000-7 000 are stationed in several regions under a bilateral agreement.

Relations between Mogadishu and Addis Ababa nosedived earlier this year after landlocked Ethiopia agreed to lease 20 km of coastline from Somaliland - a part of Somalia which claims independence and has had effective autonomy since 1991, but has failed to win international recognition.

Ethiopia offered Somaliland possible recognition in exchange for being allowed to set up a naval base and commercial port – a move Mogadishu has called illegal.

"If they do not repeal the (agreement) before the end of June, or when the new mandate of the mission is decided, all Ethiopian troops, ATMIS and bilateral, will have to go," Somalia's national security adviser Hussein Sheikh-Ali told Reuters by phone.

"Ethiopia cannot be an ally and at the same time an aggressor."

Spokespeople for the Ethiopian government and the Ethiopian National Defence Forces (ENDF) did not respond to requests for comment.

The African Union Transition Mission in Somalia (ATMIS), which is mandated by the UN Security Council, is due to fully withdraw and hand over security responsibilities to the Somali state by the end of 2024.

But the Somali government has requested several times for the withdrawal of troops to be slowed down, citing setbacks on the battlefield. The troops come from Burundi, Djibouti, Uganda, Kenya and Ethiopia.

A new, smaller peacekeeping mission is expected to be announced by the end of June, with Somalia requesting that Ethiopia not be among the troop contributing countries, according to AU and African diplomats familiar with the plan.

"Given the current political climate, it will not possible to have ENDF be part of AU-led mission," Somalia's state minister for foreign affairs Ali Omar told Reuters.