"Romania does not approve, I repeat, does not approve, in part, or in large part, of measures taken by the Italian government," Basescu was quoted as saying during a joint press conference with Berlusconi, according to the Italian translation of remarks made in Romanian.
"Roma citizens are citizens with full rights in the European Union and should be treated as such," he added.
Basescu visited Romanian gypsies in a shantytown outside Rome before his meeting with Berlusconi.
"We understand part of the measures taken by the Italian government, but we cannot agree with treatment going beyond the norms of the European Union," he had earlier said in the camp in Rome's Magliana suburb.
Tough new immigration policies in Italy have focused on Roma, whom many Italians blame for rising crime across the country.
A promised crackdown featured heavily in Berlusconi's winning election campaign in April.
The government recently ushered in a plan to fingerprint gypsies, including children, and send police into the camps to take those fingerprints by force if necessary.
Bucharest said it was concerned by the new measures and has asked that Romanian diplomatic representatives be allowed to observe what the Italian authorities say is a census-gathering exercise.
Berlusconi told Basescu during their meeting that fingerprinting to identify citizens "is a common practice in numerous European countries" and that his government plans to extend it "to all Italian citizens."
Basescu and Berlusconi appeared to agree that the issue of how to deal with the Roma was a "problem" in both their countries.
"We recognise that we have an unresolved problem at home, that of the Roma minority. We propose to the Italian government to collaborate to resolve this problem," said Basescu.
Italian Interior Minister Roberto Maroni will travel next week to Bucharest for talks with this Romanian counterpart on how to integrate the Roma population using EU funds.
The European Commission has asked Italy to report on the conditions under which its census of Roma is being conducted.
The Council of Europe's commissioner for human rights, Thomas Hammarberg, has Italy's measures signified a "worrying" step away from international law.
Rome said those concerns are "totally unfounded."