The alleged fraud was carried out through telecommunications companies and officials are investigating whether any money went to "armed groups", a statement from Spain's civil guard said.
A civil guard official said that this could mean the possible financing of Muslim extremist groups.
Spanish police have carried out several raids against suspected Muslim extremists since the March 2004 bomb attacks on commuter trains in Madrid, which killed 191 people.
Those claiming responsibility for the attack said they had carried it out in the name of al-Qaeda.
In January 2008, police arrested 15 people who were suspected of planning an attack in Barcelona.
Garzon has warned that Spain faces a "very high risk" of suffering another attack.