Spanish Foreign Minister Miguel Angel Moratinos has admitted Spain may have been a stopover for secret CIA flights.
Prisoners held at secret prisons have been moved to Guantanamo
But he said there was no evidence any crimes were committed on Spanish soil.
He was the first minister to testify before European MPs investigating claims that the CIA had ran secret jails for terror suspects in Europe.
US President Bush last week admitted that the CIA had run secret jails overseas, but he did not say where they were and they were now empty, he said.
The Spanish government is investigating more than 60 suspect flights, most of them passing through Palma de Mallorca and Tenerife.
Mr Moratinos said US authorities had given assurances that there had been no secret passengers on board planes stopping over in Spain.
However, Spanish authorities were investigating flights which could have been used to detain or fly prisoners before or after the stopovers, he said.
"Our territory may have been used not to commit crimes on it but as a stopover on the way to committing crime in another country," Mr Moratinos told a European Parliamentary committee in Brussels.
The minister said he would raise the issue at a meeting with EU foreign ministers on Friday.
The committee of MEPs has been chasing allegations of CIA secret flights and prisons in Europe for months.
The committee has heard numerous testimonies from individuals who say they were kidnapped and tortured at secret prisons.
In the light of Mr Bush's comments last week, European governments are under growing pressure to make public what the CIA was doing on their territory with or without their knowledge, the BBC's Alix Kroeger in Brussels says.
Critics of the MEPs committee have said they are motivated by anti-Americanism and lack firm evidence.
The US has defended its use of so-called rendition flights as a valuable weapon in the fight against terrorism.
Mr Bush said last week that 14 key terror suspects who had been held by the CIA have now been moved to the US naval base at Guantanamo Bay, Cuba
Those susupects include the alleged mastermind of the 9/11 attacks, Khalid Sheikh Mohammed.