Spanish courts sentenced 18 people for the bombings, which killed 191 people on two packed commuter trains on March 11, 2004, ruling that they were inspired by — but not organised by — Al-Qaeda.
But a new book by terrorism expert Fernando Reinares indicates the bombings were instigated by a senior Al-Qaeda member and the armed Islamist movement directly "approved and facilitated" them.
Reinares said that since 2008 he had been studying official documents from several countries and from Al-Qaeda itself and interviewing intelligence officials in Pakistan and elsewhere.
"The decision-making process and the terrorist mobilization that gave rise to the March 11th attacks were top-down processes and it was ultimately Al-Qaeda that approved and facilitated the attacks," he said on Tuesday.
Reinares, a researcher at the Real Instituto Elcano international affairs institute and associate professor at Georgetown University in Washington, DC, was presenting his book to journalists ahead of publication on Wednesday.
"The decision to attack Spain was taken in December 2001 in Karachi," Pakistan, and was instigated by Amer Azizi, a senior Al-Qaeda leader and member of a cell set up in Spain by the network in 1994, Reinares said.
He said the Madrid attack was initially conceived as revenge for authorities breaking up that cell but its final approval by the network's leaders in 2003 was driven by Spain's involvement in the US-led invasion of Iraq.
The attacks came just three days before general elections in Spain.
Spain's conservative Popular Party government of the time initially blamed the attacks on the Basque separatist group ETA. But many Spaniards believed they were trying to deflect attention from a possible link between the bombings and Spain's involvement in the Iraq War.
The Popular Party lost the general elections and a socialist PSOE government took power, subsequently withdrawing Spanish troops from Iraq.
A Moroccan man currently behind bars for his role in the bombings, is set for a March release.
In October 2007, Spain's National Court found Rafa Zouhier guilty of acting as a middleman in a deal which saw explosives being sold to Jamal Ahmidan, the head of the terrorist cell which staged the deadly attacks.
He is set for a March 16th release based on time served, given that he was remanded in custody in 2004. Zouhier continues to maintain he is innocent of any involvement in the attacks.