A bomb exploded at a roadside food stall on Friday about a kilometre from a hotel in Narathiwat where Thaksin was scheduled to stay briefly, wounding a TV station employee and three villagers, police said on Friday.
Earlier in the day, another bomb exploded shortly after Thaksin toured a Thai-Malaysian border town frequently targeted by suspected Muslim fighters, seriously wounding a police officer, police colonel Term Intarasa said.
The likely targets of the bomb were officials invited to the opening of a new mosque, rather than the prime minister, Term said.
Thaksin is touring southern Thailand, hoping to promote peace in a region where more than 1000 people have been killed in a 21-month Muslim insurgency.
The Thai prime minister flew south on Thursday, pledging to stay in what he called the country's most dangerous area. He slept at a well-guarded Buddhist temple.
"I am sleeping here tonight to send the clear message that this land cannot be separated. There is no liberated zone, no place where the prime minister cannot go," Thaksin said in a television interview on Thursday evening.
Thakin with Muslim children
during his tour of the south
He said used the word "terrorist" for the first time to describe the Muslim fighters. The southern provinces of Narathiwat, Pattani and Yala are the only ones with Muslim majorities in Buddhist-dominated Thailand.
Southern Thai Muslims have long complained of being treated like second-class citizens, and there have been separatist movements from time to time in the century since Thailand annexed the area.
Also on Thursday, the prime minister visited the site where five soldiers were killed a day earlier by suspected fighters dressed as Muslim pilgrims, in one of the most deadly single attacks on the military since the current insurgency escalated in January last year.
"I am sleeping here tonight to send the clear message ... There is no liberated zone, no place where the prime minister cannot go"
Thai Prime Minister
Thaksin also visited the relatives of three alleged separatist leaders to ask their help in convincing the suspects to surrender, saying he guaranteed they would be treated fairly according to the law.