The incidents, revealed in a response by the interior ministry to a parliamentary enquiry, ranged from racist graffiti to arson, stones being thrown through windows and gas pipes being slashed.
According to opposition lawmaker Albert Steinhauser who made the enquiry, 44 of the incidents that were clearly motivated by hatred.
Steinhauser told the Austria Press Agency (APA) that in 77 percent of the cases, police had not managed to track down the culprits.
"The most important thing is for the interior ministry to take these incidents seriously and make every necessary effort to investigate," he said.
He said that no one wanted a situation like in neighbouring Germany -- where the population is around 10 times larger -- which reported almost 900 such cases in 2016.
Austria, a nation of 8.7 million people, has received more than 130,000 asylum applications since 2015 following the onset of the European Union's biggest migration crisis since World War II.
The opposition far-right Freedom Party (FPÖ) has stoked concerns about the influx to boost support, with its candidate Norbert Hofer coming close to being elected president last year.
The ruling centrist coalition has taken a harder line, announcing plans to beef up surveillance, ban full-face veils in public and oblige migrants to sign an "integration contract".
It has also stepped up deportations of migrants whose asylum claims are rejected, recently offering €1,000 ($1,069) to the first 1,000 people to volunteer for repatriation.
Chancellor Christian Kern also wrote to Brussels this week looking for Austria to be exempted from an EU scheme to take in migrants relocated from hotspots Italy and Greece.
Recent studies have also shown a sharp rise in online hate speech, directed predominantly at Muslims, and suggested that Austrians' attitudes toward immigration have hardened.
The interior ministry said there were also 49 incidents carried out by migrants themselves at the shelters including violence, death threats, stalking and vandalism. No comparison figures from prior years were released.
"We have to look closely at what the causes are. We strongly suspect that trauma, experiences of war and extreme violence play a role," Steinhauser said, calling for better psychiatric care.