"There is no need to employ temporary border controls... with Italy," a joint statement from Chancellor Christian Kern and his Defence Minister Hans Peter Doskozil said.
Doskozil on Monday caused uproar by suggesting that Vienna was prepared to mobilise troops along the main Brenner mountain pass through the Alps between Italy and Austria to protect his country from migrants.
In response, Italy summoned Austria's ambassador and Interior Minister Marco Minniti warned that Vienna's "unjustified" threat could impact security cooperation between the two countries.
Kern's media office told AFP he had spoken with Italian officials on Wednesday "to remove any misunderstanding".
The United Nations' migration agency said this week that the number of people arriving in Europe after crossing the Mediterranean in 2017 had topped 100,000.
Italy has taken in nearly 85 percent -- most of them sub-Saharan Africans crossing from conflict-ravaged Libya -- and has pleaded for help from other European Union nations, saying it is struggling to cope.
Minniti said Wednesday that other EU countries should share the burden of the migrant crisis.
"It's difficult to think of an international rescue mission while leaving the problem of receiving (migrants) to a single country," he told lawmakers in Rome.
Italy will host an international conference Thursday aimed at tackling the ongoing migrant influx, as European Union ministers meet in Tallinn to discuss ways of better managing the crisis.
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