High Court Judge Baltasar Garzon had previously charged Amir Azizi with belonging to Usama bin Ladin's al-Qaida network which is blamed for the attacks.
Garzon has now expanded the charges against Azizi to include involvement in the planning of the attacks that killed some 3000 people, according to court documents.
Azizi's exact role in the purported planning meeting was not made clear. But Garzon said the meeting included September 11 figures such as the Egyptian Muhammad Atta, believed to have piloted American Airlines Flight 11 into one of the World Trade Centre towers.
Some reports have also linked Azizi to the 11 March train bombings that killed 191 people in Madrid. The Wall Street Journal on 7 April quoted an unnamed "Spanish anti-terrorism official" as saying he was the brains of the operation.
Madrid links ruled out
But Interior Ministry and court officials say they cannot link him to the train bombings.
Police re-issued a photo of Azizi on 4 April, saying he was wanted for "Islamic terrorism". The picture was released a day after seven train bombing suspects blew themselves up in an apartment rather than surrender to police who had surrounded the building.
The timing led to speculation Azizi was sought in the train bombings but officials insisted that was not the case.
The judge said Azizi was part of an extremist underground that recruited members and sent them to Afghanistan for training in bin Ladin's camps before the US invasion.
The invasion of Afghanistan, where the Taliban had granted refuge to bin Ladin, reportedly produced documents indicating Azizi had trained there using his alias, Uthman al-Andalusi.