The other four are: Douglas Feith, the former undersecretary of defence for policy; John Yoo and Jay Bybee, two justice department officials; and William Haynes, a Pentagon lawyer.
"The charges as related to me make no sense," Feith said on Saturday.
"They criticise me for promoting a controversial position that I never advocated."
Yoo, who wrote a series of secret memos that claimed the president had the legal authority to circumvent the Geneva Conventions and who is already the subject of a justice department ethics investigation, declined to comment.
The others either could not be reached or did not immediately respond to requests for comment, The New York Times said.
The officials are charged with providing a legal cover for interrogation methods such as waterboarding, which Spanish human rights lawyers say amounted to torture.
Boye said that the six Americans had well-documented roles in approving illegal interrogation techniques and abandoning the definition set by the 1984 Torture Convention, the newspaper said.
Spain can claim jurisdiction in the case because five Spanish citizens or residents who were prisoners at Guantanamo Bay say they were tortured there.
But even if indictments are eventually handed down against the US officials, it is far from clear whether arrests would ever take place.
The officials would have to travel outside the US and to a country willing to take them into custody before possible extradition to Spain.
Throughout his presidency, Bush denied the US tortured anyone.
The US has acknowledged that Khalid Sheikh Mohammed, the self-described mastermind behind the September 11, 2001 attacks on the US, and some other prisoners were waterboarded at secret CIA prisons before being taken to Guantanamo.
The Bush administration maintained that all interrogations were lawful.