"I am concerned that European countries are now adopting increasingly restrictive immigration and refugee policies," Ban said in a speech to the Austrian parliament.
"Such policies negatively affect the obligation of member states under international humanitarian law and European law."
His comments came a day after the Austrian parliament adopted one of Europe's toughest asylum laws, as the country's political leaders struggle to halt the surging far-right which is leading in presidential polls.
The hotly-disputed bill, which passed by 98 votes to 67, allows the government to declare a "state of emergency" if migrant numbers suddenly rise and reject most asylum seekers directly at the border, including those from war-torn countries like Syria.
If the mechanism is triggered, border authorities will only grant access to refugees facing safety threats in a neighbouring transit country or whose relatives are already in Austria.
Some groups including minors and pregnant women will be exempt from the rule.
The restrictions are similar to tough rules introduced by the right-wing government in neighbouring Hungary last year.
In addition, MPs also voted to restrict existing asylum laws by placing limits on the length of asylum granted to migrants and making it harder for their families to join them.
Opposition parties and rights groups slammed the legislation, with the UN's refugee agency warning that it "removes a centrepiece of refugee protection".
But Interior Minister Wolfgang Sobotka insisted Austria had no other choice as long as "so many other European Union members fail to do their part" to stop the influx.
Wedged between Europe's two main refugee routes - the Balkans and Italy - Austria received around 90,000 asylum requests in 2015, the second-highest in the bloc on a per capita basis.
More than a million people, primarily from Syria, Iraq and Afghanistan, landed in Europe last year, triggering the continent's worst migration crisis since the aftermath of World War II.
To reduce the flow, the EU recently struck a controversial deal with Ankara, under which all irregular migrants reaching Greece after March 20 will be returned to Turkey.
Although the pact has led to a sharp drop in arrivals, the International Organisation for Migration last week warned that the numbers were starting to rise again.
The crisis has boosted populist fringe parties across Europe, pressuring traditionally centrist governments to adopt a much firmer stance on migrants.