The attack came two days after the US said it had killed the chief of al Shabaab's intelligence and security wing, Tahliil Abdishakur.
"Al Shabaab attacked our base unexpectedly early in the morning today. We lost seven soldiers," Captain Ahmed Idow, a Somali military officer, told Reuters by telephone from Baidoa.
Idow said Somali soldiers killed three al Shabaab insurgents during the attack.
A spokesman for the al Qaeda-linked al Shabaab said the group had briefly seized the base and killed more than 10 soldiers. Al Shabaab often cites a higher death toll than the number given by officials.
"We fiercely attacked the military base near Baidoa," Sheikh Abdiasis Abu Musab, al Shabaab's military operation spokesman, told Reuters.
Al Shabaab is seeking to topple the Western-backed Mogadishu government and impose its own version of the so-called Islamic law in the country.