Socialist group leader Gianni Pittella has condemned the "unacceptable" decision to lift the immunity of 138 members of the Turkish Parliament.
His comments come on the eve of a debate in the European Parliament on Wednesday on the state of democracy in Turkey.
Turkey's Parliament recently approved stripping its members of immunity from prosecution, a move likely to see the pro-Kurdish opposition sidelined and ease President Tayyip Erdogan's path to stronger powers.
Erdogan has accused the pro-Kurdish HDP, the Turkish Parliament's third-biggest party, of being the political wing of militants who have waged a three-decade insurgency in Turkey's largely Kurdish southeast, and wants to see them prosecuted.
The HDP denies such links and says its parliamentary presence could be all but wiped out if prosecutions go ahead.
Lawmakers currently enjoy immunity from prosecution. The new law will allow prosecutors to pursue members of Parliament who currently face investigation: that includes 138 deputies, of whom 101 are from the HDP and main opposition CHP.
The HDP has said an overwhelming majority of its 59 deputies could be jailed, mostly for views they have expressed
Speaking in Parliament at its Strasbourg plenary on Tuesday, Pittella, an Italian deputy who leads the House's second biggest political group, described the decision to lift immunity as an "unacceptable act."
He pointed out that respect of fundamental rights is one of the conditions for a rapid introduction of visa-free travel for Turkish citizens as part of an arrangement for managing migration.
Further comment came from Greens/EFA group joint leader, German MEP Rebecca Harms, who questioned whether the EU's recently agreed visa liberalisation deal with Turkey should now go ahead.
She said, "By stripping a large group of MPs of their immunity, Erdogan is trying to 'correct' the electoral outcome in his favour. Leaving the opposition open to spurious legal challenges will both weaken it and remove a crucial critical voice from the Turkish Parliament.
"Erdogan's aim is clearly to secure the necessary parliamentary majority to allow him to change the constitution to his ends and to move towards an even more authoritarian presidential system.
"This law is targeted primarily at the HDP opposition party, which gained support from both the Kurdish electorate but also progressive liberal voters in the election.
"Its Chair has fought for a political solution to the conflict between the government in Ankara and the Kurdish minority, whereas Erdogan has refused to engage in the peace-process. Stripping many HDP deputies of their immunity could therefore further exacerbate the conflict.
"While the Greens have consistently supported progressing negotiations with Turkey and visa liberalisation for Turkish citizens, it is clear that the continuing slide away from democratic norms should lead the EU to critically assess if the basic conditions for visa liberalisation exist.
"Erdogan's latest blow against the rule of law again drives home that it is wrong for EU to rely on Turkey to solve the refugee crisis, she said.
Parliament President Martin Schulz said on Twitter the immunity move was a "blow to Turkish democracy" and that "the gulf with European norms and values is widening"
Erdogan's opponents say the lifting of immunity is part of a strategy to push the HDP out of parliament and strengthen the ruling AK Party.
The legislation has caused concern in Europe, which is trying to hold together a controversial deal with Turkey meant to stop illegal migration despite what many European politicians see as the country's deteriorating record on human rights.
Conflict between the state and the PKK, deemed a terrorist group by Ankara, the EU and United States, is at its most intense since the 1990s. Thousands of militants and hundreds of security force members and civilians have been killed since a two- year ceasefire collapsed in July.
Meanwhile, Nato has condemned a terrorist attack on Tuesday targeting a police vehicle in Istanbul, which killed a number of people, including police officers, and injured many others..
Secretary General Jens Stoltenberg said, "Terrorism seeks to undermine the very values that the North Atlantic Alliance stands for: democracy, individual liberty, human rights and the rule of law. It can never be tolerated or justified.
"Nato allies stand in solidarity with Turkey against the global threat of terrorism."