JOIN USA court in Kishoreganj in northeastern region remanded the two men, who belong to the United Liberation Front of Asom (ULFA), to three days's custody of the paramilitary Rapid Action Battalion (RAB).
The cases have been registered against Chowdhury under arms, explosive substances and anti-terror laws.
Chowdhury has different aliases like Major Ranjan, Pradip Roy, Dip Jyoti, Ranju Barai and Masud Chowdhury, New Age newspaper said Monday.
Chowdhury, 46, and his associate Pradip Marak, 57 were paraded before the media Saturday.
Chowdhury assumed a Muslim name, Masud Chowdhury, to evade detection and had been picked up by police six weeks ago, said a media report.
He had also married a local girl, a common trait among Indian militants who cross the border into Bangladesh to evade arrest.
ULFA's military wing chief Paresh Barua, believed to be in Bangladesh, has also married a Bangladeshi girl and goes by the name Zaman.
According to The New Nation, he "is probably the same Masud Ranjan Chowdhury" picked up by the police six weeks ago. He was arrested by plainclothes policemen June 6 from Rumpa Clinic in Mymensingh town.
At that time, police and the RAB had denied the arrest, the paper said. But his wife Sabitri Sangma confirmed the arrest to mediapersons.
Chowdhury's arrest was the first "official announcement" made by Bangladesh authorities of the nabbing of an Indian militant leader, New Age newspaper said.
Bangladesh authorities say Chowdhury has been heading violent operations from Bangladeshi soil since last December's detention of the top brass of the ULFA. Chowdhury is a former general secretary of the Dhubri district unit of ULFA.
Last December, the Bangladesh authorities facilitated the arrest of ULFA chief Arabinda Rajkhowa, Raju Barua and eight others of the group.
India and Bangladesh have stepped up cooperation in handling crime, militancy and terrorism since Prime Minister Sheikh Hasina took office in January last year.
The Daily Star newspaper Sunday quoted chief of RAB Intelligence Wing Lt. Col. Ziaul Ahsan as saying: "ULFA activities in India are apparently regulated by its leaders and operatives who have taken shelter in Bangladesh. Among them, Ranjan Chowdhury is now the chief as the other top leaders of the separatist group are in jail."
RAB chief Major General Hasan Mahmud Khandaker said: "We are trying to find out whether ULFA has any links with local militant outfits or has any military wing here. We are also trying to ascertain how many ULFA leaders and operatives are living here."
Commander Mohammad Sohail, director of RAB legal and media wing, said Chowdhury married a Bangladeshi and started living at Gazni village in Sherpur since 1997. He has been making frequent trips to India.
Chowdhury illegally entered the country through Kurigram district in September 1997 to meet ULFA military wing chief Paresh Barua in Dhaka, said Sohail.
In 1995, Indian law enforcers arrested Chowdhury on his way back to India from Bhutan after his meeting with ULFA general secretary Anup Chetia, who has been convicted in several cases and is now in jail in Bangladesh since 1997.