Taysir Alluni was arrested three days earlier in a storm of criticism and condemnation by the satellite news channel and numerous non-governmental organisations.
Police took Alluni to Madrid after accusing him of using his profession to enter into contact with "terrorists", most famously after recording an exclusive interview with Usama bin Ladin.
Spanish Judge Baltasar Garzon will also be investigating Alluni's connections with Imad al-Din Barakat Yarkas who was arrested on suspicion of being the ringleader of an Islamist cell which Spanish authorities dismantled in November 2001.
Garzon and Spanish state prosecutor Pedro Rubira suspect Alluni of involvement in "the organisation of, support for and infrastructure of this cell," according to the warrant for his arrest.
Spanish judge Baltasar Garzon
Spanish law allows police to detain suspects for three days without access to lawyers or family.
But the judge has extended Alluni's detention for another three days while evidence requested from other governments arrives.
Alluni is also accused of "furnishing al-Qaida with funds in Afghanistan," where he was an Aljazeera correspondent during the 2001 US-led war which brought the end of Taliban rule.
Aljazeera spokesperson Jihad Ballout criticised Spain's detention of Alluni saying it "is another inconvenience to which journalists in general and those from Aljazeera in particular fall victim".
Ballout added that Aljazeera has appointed a lawyer for Alluni and has been in contact with Spanish authorities as well as non-governmental organisations defending the freedom of the press.
Pakistani journalists and associations marched in protest on Sunday, calling from his immediate release and a halt to all forms of journalist harassment.
Alluni escaped a US bombing of
Aljazeera's office in Kabul
The Arab Human Rights Committee has released a statement denouncing Alluni's detention which it condemned as an outright violation of press freedom.
It added that the arrest dishonoured Spain and the police should apologise immediately to Alluni and his family.
Dozens of journalists, Iraqi citizens and human rights activists gathered outside the Spanish embassy in Baghdad denouncing the arrest.
Alluni, who rose to prominence during the Afghanistan and Iraq wars, is of Syrian origin but is a Spanish citizen.
He narrowly escaped death when US warplanes bombed the Kabul offices of Aljazeera during the closing days of the war to oust Taliban in November 2001 when Afghan officials advised him to leave the building.
Alluni was one of Aljazeera's eight correspondents in Iraq but was expelled by Iraqi authorities during the war.
Before that he worked as a translator during the 1990s for Spain's EFE news agency.
Spanish authorities have tracked his movements since at least October 2001, when the newspaper El Pais reported that Alluni's phone had been tapped by authorities while he was working for the agency's Arabic section.