The foreign ministry summoned the Italian ambassador to Switzerland on Wednesday to express "surprise" at raids on Swiss banks in his country.
Swiss officials told Ambassador Giuseppe Deodato that "Switzerland has cooperated to a great extent with the international community, with European Union countries as well as with Italy in particular in tax matters", the foreign ministry said in a statement.
A few hours later, Deodato, speaking on Swiss public radio RSR, said the action aimed at Swiss banks or Italian banks with Swiss ties was not meant to be an unfriendly move towards Switzerland.
He said the matter was an internal affair for Italy and a check up on its citizens, not Swiss banks.
Around 100 financial police agents on Tuesday targeted 76 offices including Italian branches of Swiss banks, Italian banks with Swiss ties and San Marino-linked banks.
Swiss President Hans-Rudolf Merz, who also heads the country's finance ministry, said the government was considering measures to protect the financial centres in Ticino, Switzerland's Italian-speaking canton where around 70,000 Italian nationals live.
Italy's parliament voted for a third tax amnesty in nine years on October 2 in attempt to repatriate funds it believes Italian tax dodgers have stashed in foreign banks.
Switzerland has complained about being singled out for tougher treatment and resents Italian police "spying" on the border with surveillance cameras. Italy says Switzerland has encouraged its citizens to dodge taxes.
swissinfo.ch and agencies