Sri Lanka's Defence Minister Gotabhaya Rajapaksa told the BBC that Pathmanathan was detained in Thailand, where he had been residing for many years.
There has been no comment yet from the rebels on Pathmanathan's arrest.
Rajapaksa did not elaborate on the circumstances surrounding the capture.
Pathmanathan was widely believed to be running the LTTE's arms and smuggling networks for years.
As the new rebel leader, Pathmanathan said the LTTE had decided to silence their guns and would try non-violent methods to achieve their goal of a separate state for the Tamil minority, BBC reported.