The European Union's executive Commission said on Thursday it regretted Slovakia's move which critics have said will damage democracy in the formerly communist country of some 5.5 million people.
Ending the special prosecution unit USP, after two decades of work, was a major pledge of the new government of Prime Minister Robert Fico, who has accused the office of bias against his party and of violating human rights.
"This (closure) is clearly not in conflict with EU law," the Justice Ministry said in a statement.
Closing the office was approved by lawmakers in a fast-track procedure that had raised EU concerns and strong criticism from the opposition and President Zuzana Caputova, who has challenged changes to the law concerning sentencing and statutes of limitations at the Constitutional Court.
Tens of thousands of Slovaks have protested the government actions.
The Commission said on Thursday it would assess the consequences of the prosecution office's closing and "not hesitate to take action to ensure respect of EU law and the protection of the EU's financial interests".
Cases handled by the office are to be handed to other prosecution branches, and the Justice Ministry said the approved law gave sufficient guarantees investigations would not be compromised.
The ministry said consultations with the Commission continue and any doubts about the changes were unfounded.
The government last week launched a planned revamp of public broadcaster RTVS in a bid to bring it under direct state control, raising concerns with EU media over democracy and freedom of expression.
(Reporting by Jason Hovet in Prague; Editing by Nick Macfie)
