The soldiers are reportedly taking over the security of an airport which was abandoned when government troops defected to the Islamic militia that controls the capital, Mogadishu, and much of the south of the country.
Witnesses said about 90 government troops went over to the Supreme Islamic Council of Somalia (SICS), the latest in a series of defections.
Earlier, residents in Awdiinle, about 30km from Baidoa said they saw 11 trucks carrying about 300 heavily armed Ethiopian soldiers pass through.
“We have seen Ethiopian troops here in Awdiinle,” a resident told Reuters news agency. “They are advancing towards Baidoa. We know these are Ethiopian troops because of their trucks and their uniforms.”
The Supreme Islamic Council of Somalia, formerly called the Islamic Courts Union, said the soldiers came at the request of the government.
Ethiopia moved troops into Somalia last month to protect the Somali government from attacks by the increasingly powerful Islamists who it says are being supplied by neighbouring Eritrea.
Both countries have denied that Ethiopian troops are in the country, but Addis Ababa has threatened to “crush” the Islamic courts if they target the transitional government.
The Islamists have refused to participate in Arab League-mediated peace talks in the Sudanese capital, Khartoum, until the Ethiopian troops pull out.
The latest deployment came as the Islamist movement announced it would organise a national forum to plan the country’s future, further bypassing the weak transitional government.
More than 14 internationally backed initiatives have failed to restore peace in Somalia, which plunged into lawlessness in 1991 after Mohamed Siad Barre was overthrown.