"Pathmanathan is in Sri Lanka and he will be questioned for international links of the LTTE", Military Spokesman Udaya Nanayakkara said.
54-year-old Pathmanathan, who had been named by slain LTTE chief Velupillai Prabhakaran as the new head of the LTTE was bought back to Sri Lanka late on Thursday via Bangkok and was being questioned, officials said.
Better known as 'KP', Pathmanathan is known to be an arms dealer and is on the wanted list of Interpol on gun running charges.
In a statement, put on its website the Sri Lankan defence ministry said Pathmanathan "had been taken into custody by the Sri Lankan law enforcing authorities".
Pathmanathan was appointed international representative of the Tamil Tigers as they made their last stand on the beaches of Killinochi, where Sri Lankan forces overran them.
He was the Tamil leader who announced the death of LTTE supremo Prabhakaran and later proclaimed himself as the head of the Tamil Tigers.
Earlier reports had said that Pathmanathan had been arrested in the Thai capital Bangkok. However, the Thai government spokesman said Pathmanthan was arrested in Kuala Lumpur and flown to Colombo via Bangkok.
"The Thai government wants to reaffirm that KP is not in Thailand nor was he arrested in Thailand, although he did used to visit the country," a Thai government spokesman Panitan Wattanayagorn said.
The arrest of Pathamanathan in Malaysia was acknowledged by the Tamil Tigers who said he had been handed over to the Sri Lankan authorities.
Soon after taking over as LTTE chief Pathmanathan had said he would use non-violent means to seek the rights of the Tamil people in Sri Lanka.
The Sri Lankan Prime Minister Ratnasiri Wickremanayake told Parliament yesterday that the authorities would not allow terrorism to take shape again in the Tamil dominated northern areas.
