In a letter addressed to Spanish Prime Minister Jose Maria Aznar on Wednesday, the channel's director Shaikh Hamad bin Thamir al-Thani urged Alluni be freed.
Madrid should give the matter the importance it deserves, he wrote.
Alluni, a Spanish citizen of Syrian origin, was arrested while on holiday in Granada last Friday. Aljazeera has appointed a lawyer to defend him.
He was taken to Madrid where he has been held in a cell in the police station in the district of Canillas, in the north-east of the capital.
Alluni shot to fame following his exclusive coverage from Kabul during the US-led war against Afghanistan. The channel's bureau in Kabul was also attacked during the war.
Spanish police sources said the reporter had been arrested on the orders of judge Baltasar Garzon as part of his investigations into militant operations.
Police say Alluni is suspected of having links to members of al-Qaida, including Imad al-Din Barakat Yarkas, alias Abu Dahdah, who was arrested on suspicion of being the leader of a militant cell which Spanish authorities dismantled in November 2001.
Alluni has categorically denied any ties to al-Qaida.
In related developments, a source close to the case said Alluni had delivered money for a wedding in Afghanistan and not "terrorist" activities.
Spain's judge Baltasar Garzon
interrogated Alluni all week
The unnamed source refuted other accusations made in the prosecutor's case, saying Alluni's acts of hospitality were wrongly misinterpreted as collaboration with al-Qaida.
Garzon was due to decide by Thursday whether to release Alluni or order him to stand trial.
The source said Alluni delivered money to people in Afghanistan and Turkey three or four times on behalf of Syrians who knew he would be travelling in the region.
Prosecutors said earlier this week that Alluni delivered $3000 to $4000 on a number of occasions.