Both countries are part of the passport-free Schengen zone and have been key transit countries for tens of thousands of refugees and migrants desperately seeking to reach northern Europe via the Balkans.
"This is about ensuring an orderly, controlled entry into our country, not about shutting down the border," she told public broadcaster Ö1.
Mikl-Leitner, a member of the conservative ÖVP party, added that the situation risked escalating as people were forced to wait in freezing temperatures for hours before being allowed to cross from one nation into another.
"We know that in recent days and weeks individual groups of migrants have become more impatient, aggressive and emotional. If groups of people push from behind, with children and women stuck in-between, you need stable, massive measures," she said.
Austria 'out of line'
However, Germany said on Wednesday that Europe's refugee crisis cannot be solved with the construction of border fences or walls.
"We do not believe that the current migrant crisis that Europe is facing can be resolved with the building of fences or walls," said government spokesman Steffen Seibert, adding that the problem could only be dealt with if Europe stood united.
Germany's Interior Minister Thomas de Maiziere has hit out at Austria for sending asylum seekers to its border without any warning, saying the neighbouring country's behaviour was "out of line".
"The behaviour of Austria in recent days was out of line. We have to complain that refugees were driven without any warning after dark to... the German border," he said.
De Maiziere said both sides have discussed the problem, and that "Austria yesterday pledged to return to an orderly process." "I expect that to happen immediately. We are in constant contact on that aspect," he added.
Previously, Austrian ministers had avoided using the word 'fence' - talking instead about the need for "special structural measures" on the border. Last week, Mikl-Leitner drew strong criticism from opposition members for saying that it was time for the EU to "build fortress Europe".
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But Defence Minister Gerald Klug, of the Social Democrats, told Ö1 radio that he supports the idea of a fence, which is necessary "in order to properly control the refugees" but that "we must not lose sight of humanity". He added that Hungary's razor-sharp barbed wire fences were not the solution.
The Secretary-General of Amnesty Austria, Heinz Patzelt, told Ö1 that fences are "a symbol of a lack of solidarity" - and that barriers would not deter refugees from trying to enter Austria.
Mikl-Leitner said in a statement sent to the media that the fence would be "solid and stretch several kilometres left and right of the border crossing", but did not give a date for when construction would begin.
She also said that 200 police officers would be trained to become special border police, and that Austria needs an additional 2,000 officers as the force is stretched to its limits.