The first blast wounded seven people and the second blast near a food stall injured nine members of a police bomb squad investigating the earlier explosion in the provincial capital of Yala.
The twin explosions on Friday came amid growing outrage over the deaths of 85 Muslim protesters in the southern region earlier this week.
The protesters died - crushed to death or suffocated - after they were arrested and crammed on to military transport trucks following a crackdown on a demonstration on Monday in the Muslim-dominated south.
The foreign ministry said three other protesters died under unexplained circumstances.
Thai Prime Minister Thaksin Shinawatra promised to find the truth behind the deaths of the 85 Muslims in army custody and punish any "wrongdoers".
"I will set up an independent commission to investigate the incident with the aim
of bringing wrongdoers to justice"
Thai Prime Minister
Speaking on national television and facing the biggest crisis of his four-year-old government, he did not apologise for the actions of his troops and denied his administration was mistreating the country's Muslim minority.
"In the course of carrying out my job under the law, maintaining law and order, protecting territorial integrity, if I do anything wrong, I am willing to be responsible," he said, speaking in Thai.
Thailand's mainly Muslim south has seethed with anger this week after 78 men suffocated to death while crammed into army trucks after a violent protest on Monday.
Thaksin, under pressure from close ally the United States to hold a full investigation, said he will appoint an independent panel of religious and legal experts, headed by a former parliamentary inspector-general, to "get the complete and true facts".
"I will set up an independent commission to investigate the incident with the aim of bringing wrongdoers to justice," he said.
"If there is something wrong with the procedures, then we will have to make adjustments to avoid future similar incidents."
Analysts say the fresh violence in the strife-torn region has damaged Thaksin's reputation ahead of a general election, but he is still widely expected to win.