Caritas, Diakonie and the Austrian Red Cross - who all provide services to refugees as part of their work - spoke out at a press conference on Monday against a change to the country's asylum law.
As of mid-May, the government will only accept cases of refugees facing threats to their safety in a neighbouring transit country or whose relatives are already in Austria.
The then Interior Minister Johanna Mikl-Leitner said the decision was in accordance with European Union law which allowed member states to take national measures in emergency situations.
Austria - which last year received one of the highest asylum claims per capita in the EU - was no longer "obliged" to accept all requests because the migrant crisis posed "a threat to public order and national security", Mikl-Leitner said.
The new rules will also force migrants to request asylum directly at the border in purpose-built registration centres, where they may be held for up to 120 hours while their application is being checked.
Charities say, however, that the government is making a “huge mistake” and the policy is only a support programme for smugglers and will lead to more deaths.
“We are talking about the abolition of asylum rights in Austria, irrespective of the degree of vulnerability,” said Diakonie Director Michael Chalupka.
The charities argued on Monday that the change in law threatens basic human rights and the use of a state of emergency without any real emergency and only for “the survival of an overwhelmed government team”, according to Chalupka.
Caritas President Michael Landau also strongly criticised the idea of only accepting asylum application in certain circumstances in an “alleged emergency”, adding that he doubts human rights would be respected in the detention centres.
“Objectivity is needed now, not doomsday talk,” he said, adding that the true meaning of human rights becomes clear in times of crisis.
Many politicians are also sceptical about the changes.
Vienna SPÖ party secretary Georg Niedermühlbichler described it as “unacceptable” and the city's integration officer Sandra Frauenberger said the law was “intolerable”.
Defence Minister Hans Peter Doskozil (SPÖ) argued however that now is the time for such measures. “If this does not happen now, than we will see a similiar situation as last year,” he said.