Somalia sent the Ethiopian ambassador from Mogadishu home for consultations on Thursday and closed consulates in the semi-autonomous region Puntland and breakaway region Somaliland, amid a dispute over Ethiopia's plan to lease coastline in Somaliland.

Ethiopia's foreign ministry spokesperson Nebiyu Tedla said Ethiopia did not have information on the matter, which was announced by Somalia's prime minister's office.

"The plain interference of Ethiopia's government in the internal affairs of Somalia is a violation of the independence and sovereignty of Somalia," Somalia's prime minister's office said in a statement.

Two Somali officials said the moves were linked to a dispute over a memorandum of understanding landlocked Ethiopia agreed on January 1 to lease 20 km of coastline in Somaliland - part of Somalia which claims independence and has had effective autonomy since 1991.

Ethiopia said it wants to set up a naval base there and offered possible recognition of Somaliland in exchange - prompting a defiant response from Somalia and fears the deal could further destabilise the Horn of Africa region.

Somalia's President Hassan Sheikh Mohamud previously called the port deal illegal and said in February his country would "defend itself" if Ethiopia were to go ahead with it.

Tensions between Mogadishu and authorities in Puntland also rose over the weekend when Puntland's state council said it had withdrawn from the country's federal system and would govern itself independently in a dispute over constitutional changes.

The move to expel the ambassador and shut down the consulates raises concerns over the fate of 3 000 Ethiopian soldiers stationed in Somalia as part of an African Union peacekeeping mission fighting against militants from al Shabaab, an al Qaeda affiliate.

In February Mohamud said he did not plan on kicking them out.