Polish military police have raided a Nato-affiliated counterintelligence centre in Warsaw in the latest of a series of moves by the country’s new rightwing government to consolidate its hold on power.

The raid took place at 1.30am on Friday at the temporary offices of the Nato Counter Intelligence Centre of Excellence. According to the Gazeta Wyborcza newspaper, senior aides of Antoni Macierewicz, the defence minister, accompanied by military police, entered the building using a duplicate key.

The centre’s night staff called the director, Col Krzysztof Dusza, but he was prevented from entering. A defence ministry spokesman said Dusza had not responded to an order to step down from the post.

Any such change of management was supposed to have been a matter of consultation with Nato and the Slovak government, which is a partner in the centre. Neither Nato nor Slovak officials could confirm whether any such consultation had taken place.

The former Polish defence minister Tomasz Siemoniak told reporters: “Nothing like this has happened in the history of Nato, that a member state attacks a Nato facility.”

The Slovak defence ministry said: “The Slovak side is following the situation in Poland very closely. Intensive consultations at various levels are currently ongoing. We expect a thorough clarification of the situation from our Polish partners.”

A Nato official said the raid was “an issue for the Polish authorities”, adding that the centre had yet to be accredited by Nato.

However, its creation was the subject of a formal signing ceremony in the US at the end of September attended by the Nato head of alliance transformation, General Jean-Paul Paloméros, ministers from Poland and Slovakia, as well as representatives from eight other Nato members sponsoring the institution.

Nato centres of excellence are not run directly under Nato command but are coordinated by the alliance as affiliated bodies cultivating expertise.

A Nato statement on the signing ceremony said the centre would be “the primary hub of Nato expertise in military counterintelligence”. The main facility in Kraków is due to be fully operational and accredited next year, but while it was being completed, the temporary offices were in Warsaw.

The raid represented an attempt by Macierewicz to wrest immediate control of the centre from Dusza, who had been appointed to run it by Poland’s former centre-right government ousted in October elections by the radical Law and Justice party.

Since then, the new ruling party has moved fast to put loyalists in charge of the intelligence and security agencies, and had its nominees sworn in as constitutional court judges in the middle of the night in violation of constitutional procedure. The party is also preparing a bill that would open up senior civil service jobs to political appointments.

“It is becoming a sad rule these days that the Law and Justice party chooses night time to introduce important decisions. Poles have bad memories of such incidents in the past,” said Michał Kobosko, director of the Poland office of the Atlantic Council, a pro-Nato thinktank, in a reference to communist declaration of martial law in December 1981.

“Poles are starting to makes jokes about what might happen the next night. But this incident is not a joke. In 200 days from now Poland will be hosting a Nato summit in Warsaw. Polish authorities should be extremely careful before undertaking any moves which might surprise our Nato western allies.”

Macierewicz is the most controversial figure in the new government. The defence minister has given credence to conspiracy theories about Jewish world domination and once accused the Solidarity leader and godfather of Polish democracy, Lech Wałęsa, of being a communist agent.

“This new government doesn’t take hostages,” said Eugeniusz Smolar, an analyst at the Centre for International Relations, adding that he thought the raid had been ordered by Macierewicz without consultation with the rest of the government. “They didn’t have to do this in this manner, that will alineate Nato partners and will be damaging to Polish standing in Nato.”