A court in Guwahati, Assam, sent Rajkhowa, his bodyguard Raja Bora and deputy Raju Baruah on 12 days' police remand, a day after they "surrendered" to Indian authorities in Meghalaya.
The three were produced before Kamrup Chief Judicial Magistrate Robin Phukan.
The Assam police had asked for a 14-day custody while the lawyer of the Ulfa leaders prayed for 10 days.
The Ulfa leaders were booked under the Unlawful Activities Act.
Huge crowds gathered before the magistrate's court to get a glimpse of Rajkhowa, Raju Baruah and Raja Bora.
Rajkhowa in handcuffs and Baruah claimed that they had not surrendered, that they would never do it, as they were taken back to the police van by personnel of the Special Operations Unit of Assam police.
Rajkhowa, who had been on the run from law for 17 years, accused Bangladesh of "betraying" him. He said talks with India cannot be held with his being in handcuffs.
Paresh Baruah, who is believed to be in Myanmar and asked Rajkhowa on Friday not to "fall into the government's trap" of dialogue, yesterday denied there was any split in Ulfa which has "full confidence" in Rajkhowa.
"We are ready for dialogue provided sovereignty for Assam is discussed," he said in an email to the media from an undisclosed location.
But Indian Home Minister P Chidambaram has ruled out talks with Ulfa unless it abjures violence and gives up the sovereignty demand.
Paresh Baruah said Rajkhowa had not surrendered but been arrested "following a deep-rooted conspiracy of the Indian government".
Extreme secrecy surrounds the place where Rajkhowa, Raju Baruah besides eight others were being held by the Assam police.
Rajkhowa, along with his wife and nine others, had arrived in Guwahati yesterday after they were handed over to the BSF reportedly by Bangladesh security forces at Dawki in Meghalaya.
Meanwhile, Ulfa General Secretary Anup Chetia was shifted to Rajshahi Central Jail from Mymensingh jail on Friday night, reports our correspondent in Rajshahi.
Sources said another leader of the United Liberation Front of Asom, Babul Sharma, was taken to Rangpur jail at the same time.
Acting Deputy Inspector General of prisons Tipu Sultan confirmed the reports of shifting, but he did not elaborate on the matter.
Security of Rajshahi jail was tightened after Anup Chetia was taken there.
Anup was arrested in 1997 in Dhaka. He was convicted in several cases and has since been in jail.
In the last few days, foreign media reported that Ulfa Chairman Arabinda Rajkhowa and a few other leaders were arrested in Dhaka and later handed over to the Indian authorities.
But on Friday, Bangladesh government dismissed such claims.
Terming the media reports baseless, Home Minister Sahara Khatun said, "Since we did not arrest him [Rajkhowa], there is no question of pushing him back."
The same day the Indian authorities formally announced that the Ulfa chairman surrendered to the Indian Border Security Force earlier in the day at Dawki in the northeastern state of Meghalaya.