Federal Police have confirmed the Department of Prime Minister and Cabinet ordered a raid on an Indigenous newspaper which published leaked cabinet documents.

The search warrant was executed this morning at the Canberra office of the National Indigenous Times.

The secret Cabinet documents allegedly related to the consequences of abolishing ATSIC.

The newspaper's editor Chris Graham has defended the decision to run the stories.

"We're not critical of the Australian Federal Police at all, they're just doing their job," he said.

"But it is mind-numbingly stupid, or breathtakingly arrogant for the Government to believe they can raid the offices of a newspaper and not spark the interest of a great many journalists, and that's precisely what they've done."

Mr Graham says he is not worried about any criminal charges.

"We would wear whatever consequences but I sincerely doubt the Government will persist on this line," he said.

"They've been exposed as being arrogant and stupid and I think they'll crawl back from whence they came rather than push this any further."