Barroso was quoted as saying that Macedonia must urgently reform its judiciary and public administration and step up the struggle against corruption and organised crime.
He also called for solving the dispute over the name of Macedonia with Greece as soon as possible.
Macedonia was granted the status of European Union candidate country in 2005, but has not yet received the green light to open accession negotiations. The main obstacles to the opening of negotiations is the Macedonia-Greece dispute over the former's name and Macedonian internal problems.
Barroso arrived in the Macedonian lakeside resort of Ohrid on Saturday after visiting Croatia, Bosnia and Herzegovina, and Montenegro on his tour of the region.