EU Migration Commissioner Dimitris Avramopoulos will raise the issue with Austria's Interior Minister, the Commission's spokeswoman told a press conference.
"The Commission is very concerned," Natasha Bertaud said.
Austrian police said construction work started Tuesday on concrete foundations for a planned control area off the northbound motorway at the Brenner pass in the Alps.
"If these plans should materialise then we will have to look at them very seriously. The Brenner pass is essential for freedom of movement within the European Union," Bertaud said.
She was referring to the passport-free Schengen zone, a symbol of European freedom and unity which has come under threat of collapse with the reintroduction of border controls to stem the massive influx of refugees and migrants in the last year.
"The reintroduction of border controls at internal Schengen borders has to be exceptional and proportionate," Bertaud said.
"So the Commission will assess any measures that are taken by the Austrian government from the perspective of the necessity and the proportionality of the measures," she said, adding that Avramopoulos will be in contact with Austria's interior minister later Tuesday.
Austria and several other EU member states have reintroduced temporary border controls along the so-called Balkans route from Greece to stem the massive inflow of migrants, many coming from war-torn Syria.
Austria is concerned that following the closure earlier this year of the Balkan trail from Greece towards Austria, a new route across the sea from Libya to Italy and then northwards will open up.
But Bertaud said: "For the time being there is indeed no evidence that flows of irregular migrants are shifting from Greece to Italy, though we have seen an increase in the numbers of people arriving to Italy."
Austria's government, which wants to slash numbers claiming asylum in the country this year to 37,500 from last year's 90,000, says it is planning additional measures at several border crossings from June 1.