"Disgrace!" and "Killers!" a small group of activists and residents shouted as Barroso stepped off his plane with Italian Prime Minister Enrico Letta in Lampedusa.
Fishermen also sounded their sirens in protest.
"They should be ashamed of themselves! They should solve this humanitarian problem!" one protester said at the fence of the local airport.
Another said: "We've been living with this for 20 years. We've had enough of death! These deaths are on the conscience of Italian and EU politicians."
An estimated 17,000 to 20,000 migrants have died during the perilous crossing over the past 20 years as they often make the journey on badly overcrowded fishing boats or rubber dinghies.
Eritrea, Somalia and Syria are the main countries of origin and the majority of arrivals are on Lampedusa, Italy's southernmost point which is closer to north Africa than to the rest of Italy.
The centre houses around 1,000 migrants, including previous arrivals, but only has 250 beds. They are being held in unsanitary conditions that were judged "unacceptable for a civilised country" by a group of parliamentarians that came to inspect it.
There have been tensions at the heavily-guarded centre in recent days as migrants -- some of whom have been sleeping in the open -- demand to be moved to other facilities on the Italian mainland.
Barroso was also travelling with the EU's Home Affairs Commissioner Cecilia Malmstroem, who has called on EU member states to beef up the Frontex border guard service to mount "a big search and rescue" operation across the Mediterranean.
The deputy head of Frontex, Gill Arias, was quoted by the Italian news agency ANSA as saying that the agency would allocate an extra 2 million euros (USD 2.7 million) to Italy but added that any other funds for 2013 had already all been used up.
