"In terms of timing and organisation, nothing has been thought through," Werner Faymann told Austrian public radio in an interview. "A lot more has to happen... There are gaps everywhere."
He said that the European Union's aim to have the "hotspots" - where migrants will be registered, fingerprinted and sorted - ready in Greece and also Italy by the end of November was unrealistic.
"Even (to be ready)... by the end of the year requires central coordination, considerably more resources, considerably more personnel," Faymann said after visiting the Greek island of Lesbos on Tuesday.
The "hotspots", agreed by EU leaders at a summit last month, are aimed at separating the new arrivals between bona fide refugees and economic migrants at their first entry point into the bloc.
Those deemed to warrant refugee status can then be relocated to other EU countries to ease the burden on Greece and Italy and to prevent the migrants from continuing northwards in an uncontrolled manner.