The officers are accused of selling foodand fuel, meant for troops, on the black market, reports say.
The Ugandan contingent head, Brigadier Michael Ondoga, is among those being investigated.
Uganda is the biggest contributor to the AU force of about 18,000.
The force, funded mainly by the United Nations (UN) and European Union (EU) is fighting the al-Qaeda-linked al-Shabab group in Somalia.
Brigadier Ondoga has not commented on the allegations.
‘Only one meal’
He was among the officers who had been recalled for allegedly “getting involved in conduct injurious” to the AU force, a Ugandan defence ministry spokesman said, AFP news agency reports.
Army spokesman Colonel Paddy Ankunda told the BBC Swahili Service that the 20 would remain suspended, pending the outcome of an investigation into the allegations against them.
The investigation followed complaints by junior officers of “unscrupulous conduct” by their superiors, he said.
This included allegations that junior officers were not being paid and foodmeant for them was being sold, Col Ankunda told the BBC.
The suspended officers would be court-martialled and dismissed from the army if found guilty, he added.
Uganda’s privately owned Daily Monitor newspaper said in a report that Ugandan soldiers in Somalia often get only one meal a day because of the alleged theft and sale of food to private companies.
Uganda’s President Yoweri Museveni had cancelled Brig Ondoga’s appointment as military attache to Kenya, it reports.
He was due to have taken the post when his term as head of the Ugandan contingent in Somalia ended at the end of the month, the Daily Monitor adds.
Uganda has more than 6,000 troops in the AU force in Somalia.
Other countries that have deployed troops to Somalia as part of the AU force include Burundi, Kenya and Djibouti.
The force has helped the UN-backed Somali government regain control of key cities and towns from al-Shabab.
However, most of southern Somalia still remains under al-Shabab’s control.
