As a condition for joining, the new members have tightened controls on their borders with non-EU nations and linked into an information exchange system for police and border guards around the EU, measures which Barroso said will boost security.
On Thursday, Slovakia and Austria launched ceremonies to mark the extension of the passport-free Schengen zone.
Alfred Gusenbauer, the Austrian chancellor, and Robert Fico, Slovakia's prime minister, symbolically cut in half a frontier barrier at the Berg-Petrzalka crossing between the two countries.
Fico annocuned: "From midnight tonight [Thursday], you can travel 4,000km from Tallinn in Estonia to Lisbon in Portugal without any border controls."
But critics say expanding the Schengen areas will encourage the flow of illegal immigrants and raise crime rates.
Many Austrians have expressed concern that lifting border controls along the 1,260 kilometres Austria shares with the Czech Republic, Hungary, Slovakia and Slovenia will bring a crime influx.
An ORF public television poll put the number of Austrians opposed to the lifting of barriers at 75 per cent.
Similar concerns have been expressed across the border in Solvakia. "It will allow more criminals to come, for example from Austria, mostly from the Turkish minority and from former Yugoslavia," said Ondrej Kralik, a Slovak policeman who has worked 11 years at various border crossing points.
While sea and land border restrictions have been lifted, air passengers flying between the old and new EU member states will continue to face passport controls, although those too are scheduled to disappear on March 30.
Britain and Ireland are not signed up to the Schengen treaty, and the EU's two most recent members, Bulgaria and Romania, are not yet allowed to join.