According to reports, Pathmanathan, who was the head of the international division of the LTTE till Velupillai Prabhakaran's death in May, was arrested in Bangkok.
Last month the LTTE has named Pathmathan as its new chief, saying the outfit will "modify" the strategies of its "struggle" but will continue to work for a "free Tamil Eelam".
The Tamil separatist outfit was virtually annihilated by Sri Lankan troops in May.
The 54-year-old new LTTE chief, who was better known as KP or Kumaran Pathmanathan, was named as the rebel outfit's international relations' head by Prabhakaran some months before he was killed.
The Sri Lankan government, earlier appealed to foreign governments to find and arrest Pathmanathan, who allegedly ran an international weapons smuggling ring.
He was the first top LTTE leader to acknowledge Prabhakaran's death in an army operation in Sri Lanka's north and had announced a "provisional transnational government of Tamil Eelam" nearly a month after Sri Lanka officially declared victory over the rebels.
Following the death of Prabakaran, there were reports that many Tamils were angry with Pathmanathan for quickly acknowledging Prabhakaran's death.
Pathmanathan is also accused as one of the main conspirators behind the assassination of former Indian Prime Minister Rajiv Gandhi.