Thailand's defence minister contradicted the police statement on Thursday and said the series of bombings in Thai tourist towns in August were not linked to Muslim separatists.
"Even though the arrested suspects were from the southern provinces this is not an expansion of the insurgency and not related to southern violence," Deputy Prime Minister and Defence Minister Prawit Wongsuwan told Reuters.
Last month, a wave of deadly explosions in the central and far south of Thailand killed four Thai people and wounded dozens, including foreigners. Experts say the bombs were targeted to the crucial tourism industry in the nation. The police said several of the bombs were detonated by mobile phone.
No group had claimed responsibility for the attacks yet but the officials have clearly ruled out any link to foreign militants.
The analysts believe that the separatist insurgents in the country's three southern Muslim-majority provinces of Yala, Narathiwat and Pattani bordering Malaysia were responsible for the attacks.
The police have arrested two suspects in connection with the tourist-town attacks and have issued several warrants after the explosions.
During periods of heightened political tension, small bombings were common in the country but such deadly incidents were very few. Tourists are rarely targeted in Thailand.
On Friday, Thailand and Malaysia agreed to consider building a border wall to combat transnational crime and smuggling.
Reports say that since 2004, more than 6,500 people have died, the majority of them being civilians in clashes between the Malay Muslim rebels and Thai security forces stationed in the area.
The series of bombings took place just days after Thailand approved its new military junta-backed constitution.
However, Prawit said violence in the three southern provinces had decreased by 60 percent since the junta took power.