Now there can't be any doubts about that,' he said.
Pathmanathan had been known as the rebel movement's main arms procurement agent and had been operating in Thailand and other countries, although his recent whereabouts had not been known.
He is also wanted by India in connection with the assassination of former Indian prime minister Rajiv Gandhi in 1991.
'We are willing to consider any request from any country keeping with the conventions or treaties we have with them to allow Pathmananthan to be questioned,' Rambukwella said.
He said that Pathmanathan was being questioned by local defence authorities but did not disclose details of confessions or statements made by the rebel leader.
Pathmanathan has a Thai wife and in the past had often been in and out of Thailand.
In a statement issued last month, the LTTE rebels said they had set up a new headquarters and formed sector-based working groups and an executive committee to continue their struggle for a separate homeland for Sri Lanka's minority Tamils. They did not say where their new headquarters was located.
The Sri Lankan government has vowed not to allow the rebel movement to rise again after it killed its entire leadership to end a 26-year-long armed conflict in the northern and eastern parts of the country.
About 10,000 rebels are said to have been arrested or surrendered to security forces, and some of them are currently undergoing rehabilitation, the government said. Others are to be charged with crimes.