"This decision is extremely regrettable but we will continue our contacts and mobilise support to obtain Taysir Alluni's freedom," spokesman Jihad Ballout said in Doha on Friday.
The spokesman made it clear that Aljazeera was in no doubt about the innocence of its Syrian-born reporter, who also holds Spanish citizenship.
"We are convinced of Taysir Alluni's innocence and we have full confidence in the impartiality of Spanish justice," he said.
Aljazeera Chairman Shaikh Hamad bin Thamir al-Thani has written to Spanish Prime Minister Jose Maria Aznar to press for Alluni's release.
Aljazeera's journalists have signed a petition of support for their colleague, and anchormen and women appear on the screen wearing a badge carrying his picture.
Alluni's exclusives are being replayed and an open forum enables viewers to express their own solidarity with the detained journalist.
"This is much more than a disappointment," the channel's Brussels correspondent Ahmad Kamel, in Madrid to monitor developments, said on Thursday following the decision to keep Alluni in custody.
"We are convinced of Taysir Alluni's innocence and we have full confidence in the impartiality of Spanish justice"
"There will be consequences, there will be demonstrations in the Arab world and appeals to boycott tourism (in Spain) and Spanish products," he said.
A Spanish judge on Thursday ruled that the journalist should remain in custody pending further investigations into the purported links.
Judge Baltasar Garzon said he believed Alluni had helped to structure al-Qaida "at national and international level by financing, controlling and coordinating ... this criminal organisation".
Garzon's conclusions, contained in a 25-page written summary, showed he was convinced after interviewing Alluni and after reading material from foreign intelligence sources that there was sufficient reason to keep him in detention pending charges.
Garzon excluded any "direct relationship" between the reporter and "the most serious acts" of "terror" which al-Qaida is alleged to have carried out.
But he said he had concluded that al-Qaida was still active "thanks to sleeper cells" whose members had to be "neutralised".
The 56-year-old Alluni found fame for exclusive reporting from Afghanistan during the US-led invasion on the Taliban launched in October 2001, interviewing Bin Ladin and later reporting from Baghdad on the war in Iraq.
Police suspect Alluni of having links to members of al-Qaida's network, including Imad Eddin Barakat Yarkas, alias Abu Dahdah, who was arrested on suspicion of being the ringleader of an Islamist cell which Spanish authorities dismantled in November 2001.
Garzon wants to neutralise
al-Qaida sleeper cells
Alluni has denied any links to the cell, which is suspected of having helped to prepare the September 11 attacks, although US authorities have not applied for his extradition.
Alluni was arrested last Friday while on holiday in Granada, where the reporter has a family home, and taken to Madrid where he remains in detention.
Under Spanish law Garzon had until Thursday to either release him or decide there was sufficient evidence to keep him in custody.
Once a member of the Muslim Brotherhood, Alluni survived a US bombing of Aljazeeera’s office in Kabul in November 2001 before leaving Afghanistan when the Taliban government collapsed.
He was to relive the same scenario in Baghdad less than two years later, when US fire on the station's office in the Iraqi capital claimed the life of one of his colleagues.