Ethiopian troops, estimated at about 3,000, were meant to prop up Somalia's transitional federal government, but the internationally backed authorities never succeeded in asserting their power on the country.
Last month Addis Ababa announced it would pull its troops out by the end of the year, causing concern among Amisom and the UN, which urged immediate talks aimed at convinving Ethiopia to keep its forces in Somalia a little longer.
"Ethiopia accepted it had a moral obligation to Amisom and it would do whatever necessary to see that its withdrawal did not harm Amisom," the Ethiopian foreign ministry statement said on Saturday.
"This did not imply any delay in withdrawal but might allow for some flexibility in terms of a few days, if necessary, but this would be for Amisom to assess."
Following the removal of the Islamic courts, al-Shebab, the group's former youth and military wing, has waged an armed campaign against Somali government troops and Ethiopian forces.
Some Islamic Courts' Union factions have signed a peace pact with the Somali government, brokered in Djibouti, but no deadline has been set for the deal and anti-government groups inside Somalia have rejected the pact.
Ethiopia has also cast some doubt on the possible agreement, with the foreign ministry statement saying that the Djibouti process "looks unlikely to make a breakthrough".
Since Ethiopia said it was pulling out of Somalia, al-Shebab has closed in around Mogadishu after taking most the country, leaving government and AU troops to control only a handful of locations.
On Saturday, al-Shabab was reported to have taken control of the town of Gurael, 370km north of the capital Mogadishu, after fighting that killed at least 13 people and wounded dozens of others, residents said.
Locals said the group took the town after three days of fighting with a government-allied Sunni group in the area.
The battle began after al-Shabab fighters arrested a local Quran teacher of that group, they said.