Somalia's AU force, from Uganda and Burundi, numbers about 3,200
Ethiopian Prime Minister Meles Zenawi has told parliament African Union peacekeepers in Somalia want to leave.
He said Ethiopian troops, due to pull out of Somalia at the end of the month, would cover their withdrawal.
The AU force, from Uganda and Burundi, had been expected to stay and even beef up its presence to make up for the planned Ethiopian pull-out.
Ethiopia went into Somalia two years ago to help government forces drive Islamist forces from the capital.
But different Islamist forces have been gaining ground in recent months and now control much of southern Somalia once more.
The BBC's Elizabeth Blunt in the capital Addis Ababa says Mr Meles dropped his bombshell about the African Union (AU) peacekeepers while taking prime minister's questions in parliament.
He said those governments had already informed Ethiopia they did not want to stay on after the Ethiopian forces left and the AU had asked for security and support in order to ensure safe passage for the Ugandan and Burundian troops.
Neither country has given any public indication that it wants to withdraw its troops from the beleaguered Amisom force, which numbers about 3,200.
The prime minister told MPs that the 3,000-strong Ethiopian force was only staying in Somalia so that the AU troops could finalise preparations for their departure.
He said they would leave as soon as the AU troops were ready to go, provided that that they left as quickly as possible.
"They have already informed us that they would want to withdraw before we do, and we are only waiting for ships and planes to arrive in Somalia in order for them to pull out," Mr Meles said.
"At this time, we are looking into every aspect of our withdrawal. The main issue now is to ensure that Ugandan and Burundian peacekeepers pull out safe and sound."
Uganda's deputy Foreign Minister, Okello Oryem, has reportedly denied Mr Meles' statement.
"This is absolutely not true and this is contrary to everything we have said. Our position has always been that if Ethiopia pulls out of Somalia, we will increase our presence there," he told the AFP news agency.
Our correspondent says if the Ethiopian prime minister's statement is true, Somalia would be facing what the head of the AU Commission, Jean Ping, has described as the worst possible scenario.
Islamist forces again control much of southern Somalia
Somalia's fragile transitional government would be left facing a growing insurgency with only an assortment of clan militias and newly trained recruits to defend it.
This statement comes just as the United Nations Security Council is due to consider a US proposal to send a full UN peacekeeping force to Somalia - something the AU has been pressing for.
The threat of all the African forces pulling out together might help to concentrate minds in New York, and make the adoption of such a resolution more likely, says our correspondent.