Tom Adhikary and Nilambar Rajbanshi, vice president and finance secretary, respectively, of militant outfit Kamtapur Liberation Organisation (KLO), were arrested Sunday along with an associate close to the India-Nepal border near here, police said.
"Adhikary and Rajbanshi were arrested by Special Operations Group personnel at Lichu Bagan village (in northern West Bengal's Darjeeling district) at 1.30 p.m.," Siliguri Police Commissioner Jag Mohan told IANS.
A total of 50 SIM cards, some mobile phones and a motorcycle were seized from them.
There are a number of cases of subversive activities against the duo, including the Bajrapara blast in Jalpaiguri district in which six people were killed in December.
They would be presented in court Monday.
Police had launched a massive hunt for Adhikary, especially after the Bajrapara blast.
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Inspector General of Police (North Bengal) Jawed Shamim said the two KLO leaders could have links in several extortion cases.
Police confirmation of the two arrests came nine days after reports from Nepal that authorities in the neighbouring country had nabbed them at Bhadrapur, headquarters of Jhapa district. Bengal police had then described the reports as "rumours".
Blamed for a string of attacks in northern West Bengal, the KLO has been demanding a separate Kamtapur state comprising six districts - Cooch Behar, Darjeeling, Jalpaiguri, North and South Dinajpur and Malda - of West Bengal and four districts - Kokrajhar, Bongaigaon, Dhubri and Goalpara - of Assam.