The Budapest-based Okotars Foundation and two related NGOs that together administrate aid from Norway to local civil organizations were forced to hand over documents to auditors from the Government Control Office (KEHI).
Last week Hungary's right-wing government led by Prime Minister Viktor Orban said it would audit the Norway funds to clarify "whether or not there were any grounds for government suspicion" Norway was supporting organizations, including Okotars, with links to political parties.
Last week the government published a list of 13 groups supported by the Norway grants - including minority rights groups, corruption watchdogs and an investigative journalism website - which it said are "tied to the political
A statement from the Norwegian embassy in Budapest last week however said it was not the responsibility of Hungary to audit the funding as it does not include any monies from the Hungarian state budget.
"We reject all allegations of supporting, financially or otherwise, any party political activity in Hungary," the letter added.
"This is all about (governing party) Fidesz wanting exclusive authority to decide who gets how much," Okotars CEO Veronika Mona told Hungarian media last week.
Since a 1994 agreement with the EU, the three non-EU states of Norway, Iceland and Liechtenstein have donated aid funding to poorer EU members to reduce social and economic inequalities in return for access to EU markets.
During the 2009-2014 period, Norway has allocated €153.3 million($208.5 million) to Hungary, of which around €12 million has been spent to date on over 100 groups and projects.
In April, the executive European Commission separately threatened to suspend funding payments over its concerns about how Hungary distributes EU aid.