European migration commissioner Dimitris Avramopoulos sent the complaint in a letter to Austria's Interior Minister Johanna Mikl-Leitner who said Wednesday the country would cap the daily number of asylum claims at 80.
"Such a policy would be plainly incompatible with Austria's obligations under European and international law," Avramopoulos said in a copy of the letter obtained by AFP.
Avramopoulos cited the European Convention on Human Rights, the Geneva Convention and the Charter of Fundamental Rights of the European Union.
"Austria has a legal obligation to accept any asylum application that is made on its territory or at its border," the letter said. "I would urge you to reconsider the unilateral measures which you are proposing."
Mikl-Leitner said her government had no choice but to introduce the measures taking effect from Friday because Austria is among the EU countries most under strain from the unprecedented migrant influx and is "reaching breaking point."
The move came a day after Vienna said it would step up controls at existing checkpoints along its southern frontier with Italy, Slovenia and Hungary to curb the influx of migrants and refugees trekking up along the Balkans.
The daily limit on asylum claims is in line with Austria's announcement last month that it would only take in 37,500 asylum-seekers this year -- sharply down from the 90,000 it accepted in 2015.
Since January, the country of nearly nine million has already received 11,000 asylum claims, or around 250 a day.
The government has not yet specified what it plans to do once the annual quota is reached.