Three bombs went off in the business area of the city of Yala around lunchtime, they said, adding the devices may have been placed in a car and a motorcycle.
Yala Governor Detrat Simsiri told Thai television that many of the injured were hit by the third bomb, hidden in a car, as they gathered at the scene.
He later told Thai television that the situation was back to normal, but that nine people had died and 23 remained in hospital. More than ten houses had been damaged.
In Pattani province, a small bomb exploded in a food shop, slightly injuring a police officer, police said.
In a separate incident, an explosion caused a fire at Lee Gardens Plaza hotel in Hat Yai district in Songkhla province.
Some local officials attributed the explosion to a gas leak in an underground food shop but Thai media reported others as saying it could have been a bomb.
More than 300 people were hurt, most of them suffering from smoke inhalation. Channel 9 television reported five people had been killed.
More than 5,000 people have been killed since a shadowy, decades-old separatist rebellion resurfaced in January 2004 in Muslim-dominated Yala, Pattani and Narathiwat provinces.
The region, which was part of an independent Malay Muslim sultanate until annexed by Thailand in 1909, has been plagued by almost daily bombings and shootings ever since and the military has made little progress in quelling the unrest.
