The European Parliament, in a resolution approved by 496 of the 630 lawmakers who voted, said the changes needed more scrutiny and called on the European Commission to take action "to safeguard the rule of law and judicial independence".
Prime Minister Robert Fico's leftist, populist government, in power since October, unveiled the legislative changes in December and has faced near-weekly protests led by pro-Western liberal and conservative opposition parties.
The opposition says the reforms would protect allies of the current government from facing prosecution, and would put EU funds at risk if deemed to undermine the rule of law - an issue that has pitted Poland and Hungary against the European Union.
The Commission and the United States have already raised objections while Slovak President Zuzana Caputova has threatened to veto the legislation, although Fico's government will be able to override her move.
The EU parliament's resolution said the criminal code amendment and the dissolution of the special prosecutor's office (USP) - which has handled major corruption cases for two decades - "threatens the integrity of judicial processes, undermines the European Union's fight against fraud and jeopardises the protection of the EU's financial interests."
The EU's justice commissioner Didier Reynders said in mid-December the Commission could take action if criminal law changes violate EU laws.
Fico hit back at the resolution on Wednesday, calling it "interference" in domestic politics and saying Slovak opposition politicians in the European Parliament pushed it and spread "nonsense and untruths" about Slovakia.
"Political opponents, opposition deputies home and abroad are standing against us, prepared to make any dirty tricks in the political fight," Fico said.
"There needs to be a quite decisive, hard, but democratic response, and I think it is time for the government to stand up to these dirty attacks," he said in a video posted on his Facebook account.
The government's plan also includes limiting protection for whistleblowers and reducing sentences for financial crimes.
The USP opened a number of cases against business leaders, judicial and police officers, following a 2020 election win by parties promising to weed out graft.
While in opposition, Fico himself had faced police charges, later dropped.
Fico returned to power for a fourth time after a September election and has accused the USP and its leader Daniel Lipsic, a former justice minister in a non-Fico government, of being politically biased against his SMER-SSD party.
(Reporting by Jason Hovet and Jan Lopatka in PragueEditing by Ros Russell and Toby Chopra)
