The Shabelle Media Network reported some guards were involved in the Sunday escape.
Baidoa, about 155 miles from Mogadishu, the country's capital, is largely controlled by Somali government forces working with Ethiopian troops.
Abdifatah Ibrahim Gesey, governor for the Bay region, told Shabelle local authorities began a search soon after the inmates fled.
Somali government forces have been conducting security operations in Baidoa, a city once controlled by al-Shabaab's fundamentalist militants.
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