"I am extremely critical," Johanna Mikl-Leitner told ORF public radio from Brussels ahead of a two-day meeting of EU interior ministers to chew over the proposed agreement.
"I am seriously wondering whether we are taking ourselves and our values seriously or if we are throwing them overboard," she said.
The mooted deal between Ankara and Brussels, discussed at an EU summit on Monday and due to be finalised on March 17th-18th, would see Turkey take back all illegal migrants landing in Greece.
Ankara proposed an arrangement under which the EU would resettle one Syrian refugee from camps in Turkey in exchange for every Syrian that Turkey takes from Greece, in a bid to reduce the incentive for people to board boats for Europe.
In return though, Turkey wants billions of euros in aid, visa-free access to Europe's passport-free Schengen zone and a speeding up of Ankara's efforts to join the EU - demands that go too far for some.
In addition, questions have been raised over the legality of the plans as well as the desirability of doing a deal with a country that critics say has had a shaky human rights record, not least regarding the media and its Kurdish minority.
Mikl-Leitner noted that only a few days before Monday's summit, Turkish police raided the offices of daily newspaper Zaman to impose a court order placing it under administration, dispersing protesters with tear gas and water cannon.
"I think it's questionable if Turkey takes control of a newspaper critical of the government and then turns up here (in Brussels) three days later and puts a wish list on the table," she said.
"And then Turkey is rewarded with discussions about bringing forward visa liberalisation," she said, suggesting that any deal with Ankara should include a "termination clause".
Turkey deal follows closure of Balkan route led by Austria
The deal with Turkey was struck in part because of the huge numbers of refugees now left trapped in Greece.
The situation became critical after Austria's introduction of a refugee cap of 37,500 for this year set off a chain of border controls throughout the Balkans.
With Austria's desire to close the Balkan route for migrant and refugees now fulfilled, Mikl-Leitner said in a separate interview with Germany newspaper Die Welt that the "clock will not be turned back".
She said: "My position is clear - the Balkan route will remain closed, and permanently."