"There was nothing, absolutely nothing... everything had been wiped," Mr Zapatero told a raucous session of the parliamentary commission. "There is nothing from March 11 to March 14 in the prime minister's office."
Mr Zapatero, whose Socialists won a surprise election victory three days after the bombings, said the incoming government had been left the bill for the erasing.
The newspaper El País reported yesterday that the job cost €12,000 (£8,200) and included erasing all email records.
Mr Zapatero accused Mr Aznar's conservative People's party government of having tried to fool Spaniards into believing the armed Basque group Eta, not radical Islamists, carried out the attacks. "It was massive deceit," he said.
He said Mr Aznar's government began deliberately misleading Spaniards from the afternoon of the attacks, when police found that the explosives in the bombs were not, as suspected earlier in the day, of the kind habitually used by Eta.
Mr Zapatero said the attacks revealed a series of security failings that had allowed the Islamist bombers to plant a dozen bombs on the morning rush-hour trains.
He said a lack of coordination between Spain's two main police forces, failures in the control of mine explosives, and a lack of police dedicated to Islamist terrorism were to blame.
The protesters, spreading the word by text messages, convened rallies at which they accused Mr Aznar's pro-US government of lying and of making Spain an al-Qaida target by backing the Iraq war.
"We did not know about, plan, participate in, instigate or support the demonstrations," Mr Zapatero said.
Eduardo Zaplana, the People's party's representative on the commission, accused Mr Zapatero of giving, at the least, implicit support to protesters.
"You still do not dare condemn such a shameful and anti-democratic act because you were the beneficiary of it," he said.
In a thinly veiled attack on his predecessor, who appeared before the same commission two weeks ago, Mr Zapatero condemned critics who accused Spaniards of cowardice for voting out the People's party.