The investigation into the bombings that killed 191 people and wounded more than 1,800 has focused on the Moroccan Islamic Combatant Group.
The court documents identify Sarhane Ben Abdelmajid Fakhet as "leader and coordinator of the different people implicated" in the attacks.
Sarhane was one of six men named on international arrest warrants issued by Judge Juan del Olmo. Others were Moroccans Jamal Ahmidan, alias El Chino; Said Berraj; Abdennabi Kounjaa, alias Abdallah; Mohammed Oulad Akcha, and his brother Rachid Oulad Akcha.
Del Olmo's documents said all are wanted for murder and belonging to a terrorist group.
Moroccan Jamal Zougam, already jailed and charged with mass murder, had been seen as the prime suspect so far.
Zougam has been linked to members of an al Qaeda cell in Spain. Police traced a cell phone found attached to an unexploded bomb in one of the targeted trains, to the shop he ran in Madrid.
The document said Moroccan suspect Berraj met with three al Qaeda suspects in Istanbul in October 2000 and had ties with Basel Ghayoun, a Syrian who is already jailed on charges of mass murder and belonging to a terrorist organization in connection to the Madrid attacks.
Berraj left his home March 9 and told people March 12 that he was leaving Spain reportedly to attend the funeral of a sister in Morocco, the documents say. Subsequent police investigations showed he does not have a sister.
Interior Minister Angel Acebes said the investigation was focusing on the Moroccan Islamic Combatant Group, a forerunner of Salafia Jihadia, which Morocco blamed for last year's Casablanca bombings. Those attacks killed 33 people and 12 suicide bombers.
Two days after the attacks, police found a videotape in which a man claiming to speak on behalf of al Qaeda said the group carried out the bombings in reprisal for Spain's collaboration with the United States and for "crimes in Iraq and Afghanistan."
French private investigator Jean-Charles Brisard said last week that Abu Musab al-Zarqawi, a Jordanian linked to al Qaeda and suspected of heading a terrorist network in Iraq, is now believed to have masterminded the Madrid bombings.
Brisard is an internationally known counterterrorism expert who has testified before the U.S. Congress and represents some family members of victims of the Sept.11 terror attacks on the United States.
Police believe some of the chief perpetrators are already in custody.
Spanish police are holding 19 people, 14 of whom have been charged. Excluding Otman El Gnaout, a detainee whose nationality has not been announced, there are 11 Moroccans or Moroccan-born Spaniards, two Indians, two Spaniards and three Syrians in custody.
Four suspects were to have been brought before del Olmo on Thursday but the session was postponed until Friday. The four are El Gnaout, Syrians Walid Altaraki and Mohamad Badr Ddin Akkad, and Moroccan Fouad Almorabit, who had been questioned and released Tuesday and was re-arrested Wednesday.
Del Olmo has also ordered the reappearance Friday of Spanish detainee Antonio Toro Castro, brother-in-law of a Spaniard already charged with supplying dynamite to the bombers.