A Buddhist couple in their 40s were killed after their house in Songkhla province was fired upon.
Two other Buddhists were seriously injured in the attack.
Surayud's government has resolved to end the bloody uprising ravaging the provinces of Yala, Pattani, Songkhla and Narathiwat, and upon his appointment as prime minister, he offered an apology to local Muslims for past government wrongdoing.
But his visit to the region on Saturday – in which he reiterated his commitment to forging a peaceful solution to the unrest – coincided with the ambushing of police patrols and torching of a government school by the suspected fighters.
More than 1,800 people have been killed in three years of unrest in the southern provinces.
Thailand's government has periodically accused Malaysia of harbouring Thai fighters in the northern states which border Thailand, a charge the Malaysian government has denied.