Austria's president has demanded explanations over police raids targeting offices and staff of the main domestic intelligence service, in a case that has stoked concerns about the far right's control of the Interior Ministry.

The anti-immigration Freedom Party (FPO), the junior partner in the coalition government led by Chancellor Sebastian Kurz's conservatives, controls the Interior, Foreign and Defense ministries. That has prompted its opponents to question how it will handle the sensitive information those departments hold.

Last week, the police raided the offices of the BVT domestic intelligence service and searched the homes of some BVT staff members as part of an investigation into suspected misuse of their office by some employees.

Such raids are already unusual, but Austrian weekly Profil and newspaper Der Standard jointly reported this week that they were carried out by a police unit not normally responsible for such operations and which is headed by a member of the FPO.

One of the BVT officials targeted heads a unit specializing in "extremism", the media said. A hard drive containing information on organizations including right-wing groups such as fraternities that are often close to the FPO was copied and seized in the raids, they added.

"The actions surrounding the ... BVT are extremely unusual and irritating," President Alexander Van der Bellen said on Twitter on Friday. "I expect the departments responsible to provide a quick and thorough explanation."

'Fake News'

The Interior Ministry dismissed the media reports.

"The story constructed by the media that the Interior Ministry obtained or wanted to obtain access to data on right-wing extremism with a (police) unit headed by a member of the FPO is in the realm of 'fake news,'" it said in a statement issued late on Thursday.

The police unit in question normally deals with street crime.

The case has already set off a political storm, with opposition parties also demanding explanations.

"The whole thing is outrageous. It stinks to high heaven," the leader of the liberal Neos party, Matthias Strolz, told state broadcaster ORF.

The leader of the Social Democrats, Christian Kern, said: "Trust in the security apparatus has been shaken drastically."

The secretary general of the Justice Ministry, which is controlled by the conservatives, said on Friday no official files on extremist groups had been seized in the raid on the home of the BVT official who headed that department.

"The extremism data... has not been seized," Christian Pilnacek told reporters, adding that only personal files were taken. He said a prosecutor was present at each raid and the police had not had access to the files after they were seized.

However, the Justice Ministry has requested explanations from the anti-corruption prosecutors' office that jointly ordered the raids, Pilnacek said. Questions included why that particular police unit was chosen, he added.