Interior Minister Johanna Mikl Leitner plans to build a new fence with Hungary and also help Bulgaria reinforce its borders to Greece, it has emerged.
Mikl Leitner said that 1.1 million migrants could seek to enter northern Europe through Bulgaria after Macedonia closed its borders.
She said stronger borders were needed across the Balkans in case the EU Turkey deal did not stop an unprecedented influx of migrants.
Austrian President Heinz Fischer said he thought there was only a 35 to 50% chance of the EU deal functioning.
Critics of the deal say it has not presented a realistic or effective plan to reduce migrants.
After the first day of the implementation of the deal, the number of migrants in Greece rose to 50,000.
A record two million migrants entered Germany last year according to official figures.
About 860,000 foreigners left Germany, resulting in record net immigration.