Announcing the move on Tuesday in Madrid, Interior Minister Jose Antonio Alonso said the matter could damage relations between Madrid and Washington.
He told Teleconco television that using Spanish airports for secret flights to transport terrorist suspects was "a serious and intolerable issue" and one which could affect "the level of relations between the two governments."
El Pais, a Spanish newspaper, said CIA aircraft carrying prisoners have made at least 10 stops in the Balearic Islands in the Mediterranean between 22 January 2004 and 17 January 2005.
A CIA spokeswoman said the agency had no comment on the report, which Alonso said the Spanish government was looking into.
Separately, a Pentagon spokesman said he was unaware of the report.
"We typically don't talk about the movement of detainees except when they are being transferred or released to another country," said Bryan Whitman. "We don't typically talk about the transit for security reasons."
He said prisoner transfers were "done with a lot of global support out there.
Interior Minister Alonso: The
issue is serious and intolerable
"I don't know all the arrangements; but we clearly have arrangements with countries all across the globe that support the global war on terror," he said.
"I'm not going to get into the specifics of any particular country and our arrangements with them," he added.
The US embassy in Madrid refused to comment on what it termed "such a sensitive issue".
When informed of the report, the main branch of the Spanish secret service, the National Intelligence Centre, asked the CIA not to use Spanish airports for ferrying prisoners, El Pais said, quoting unidentified government sources.