Hamad Amin Sadiq, a Lashker-e-Taiba activist described by Pakistani authorities as the "main operator" behind the Mumbai incident, to the custody of the FIA for 15 days.
There was no official word on the status and whereabouts of five other suspects, who the interior ministry chief Rehman Malik had said were in the custody of authorities.
Though Malik had not named these suspects during a news conference last week, sources told PTI they included senior LeT operatives Zakiur Rehman Lakhvi and Zarar Shah, who have reportedly been named in the Indian dossier submitted to Islamabad.
Sadiq was remanded to the FIA's custody by Judge Kahut during proceedings held in a makeshift court set up in the high-security Adiala Jail in Rawalpindi.
Sadiq was brought to the prison in an armoured vehicle and his face was covered with a mask. The media was not allowed to photograph him.
In its First Information Report, the FIA filed charges against Sadiq under the Anti-Terrorism Act, Pakistan Penal Code and Prevention of Electronic Crimes Ordinance.
FIA Inspector Zahid Akhtar and special public prosecutor Chaudhry Zulfiqar told the judge that authorities wanted information about Sadiq's accomplices involved in the Mumbai incident.
The officials told the judge that Sadiq was an active member of the LeT and was accused of facilitating and abetting the Mumbai attacks in collusion with other suspects.
Official documents presented in court said Sadiq, who hails from Rahim Yar Khan in southern Punjab province, was arrested in Faizabad area of Rawalpindi on Sunday.
However, interior ministry chief Malik had said during his news conference that Sadiq was arrested much earlier in Karachi.
Media reports on Saturday had said that an anti-terror court had remanded at least six suspects to the custody of the FIA. Judge Kahut has taken exception to these reports and told reporters his court could issue a legal notice in this regard.
Diplomatic sources indicated that Pakistani authorities were deliberately being vague about the status of the suspects due to security concerns and ongoing investigations aimed at uncovering more details about the planning of the Mumbai attacks.
The sources also said Western diplomats, including those from the US, had been told by Pakistani authorities that the suspects would be brought to trial in an anti-terror court.
The authorities kept the media guessing about the presentation of the suspects in court on Friday and Saturday before finally producing Sadiq before the judge in the makeshift court within Adiala Jail yesterday.
Though a special cell has been arranged at Adiala Jail for the suspects, prison Deputy Superintendent Muhammad Feroze Kilyal said they had not been brought there.
FIA officials and the interior ministry spokesman have declined to comment on the status of the suspects and the probe into the Mumbai attacks, saying they had been directed by their seniors not to speak to the media on these issues.
Pakistan last week filed formal charges against nine suspects linked to the Mumbai attacks, including Ajmal Amir Kasab, the lone terrorist captured in India.
Interior ministry chief Malik said six of the suspects are in the custody of Pakistani authorities while two others had been identified but were still at large.