Croatia on Friday confirmed violent migrant pushbacks as Greece promised to probe fresh reports of similar rights breaches on its border following pressure from the European Union.

Investigations published Wednesday in several European media used video recordings and documents to show an alleged orchestrated campaign by special police units to forcibly turn back migrants arriving in Croatia, Greece and Romania.

Videos reportedly made at Croatia's border with Bosnia in June showed men in balaclavas beating migrants with sticks and pushing them back to Bosnia.

A probe of a special team established that "people from the footage are members of the special police", police chief Nikola Milina told reporters in Zagreb.

Three of the officers have been identified and suspended for serious dereliction of duty, he said.

"Our interest is that this case be completely clarified," he said.

Greece's response was more measured.

"Obviously the Greek authorities will investigate such claims," Greek Migration Minister Notis Mitarachi told an EU meeting in Luxembourg.

"Every claim made is investigated by the judiciary, and by our internal audit."

The EU has expressed serious concern over reports of violent migrant pushbacks
The EU has expressed serious concern over reports of violent migrant pushbacks AFP / ARMEND NIMANI

Croatia lies on the so-Balkans route, used by migrants heading towards Western Europe as they flee war and poverty in the Middle East, Asia and Africa.

They enter the country mainly from Bosnia.

Human rights groups and independent media regularly accuse Croatian police of beating migrants with metal sticks, batons and pistols before sending them back to Bosnia.

Zagreb regularly rejects such allegations.

EU internal affairs commissioner Ylva Johansson met Thursday with ministers from Croatia and Greece after saying she was "extremely concerned" by the reports.

Johansson said she had received assurances that the Croatian authorities were taking the issue "very seriously" and would open an investigation immediately.

"My discussion with the Greek minister was different, and I have made clear that I will not accept that Greece does not do the investigations on this," she said.

"We have to protect our external borders, but we also have to protect our values."

Minister Mitarachi had denied the alleged pushbacks and refused to "apologise" for what he called Greece's attempts to dismantle human trafficking networks.

He criticised the EU for not doing more to enforce an agreement with Turkey meant to see Ankara prevent migrants crossing into the bloc.