Merkel spoke on the phone with President Karolos Papoulias, who failed this week to convince political leaders to form a government after an inconclusive May 6 election, meaning the vote will be held again on June 17.
"(Merkel) relayed to the President (Karolos Papoulias)thoughts about holding a referendum in parallel with the elections on the question whether Greek citizens wish to remain in the euro zone," Greek government spokesman Dimitris Tsiodras said in a statement.
Greek parties backing the country's international bailout failed to win a majority on May 6. European Union leaders and officials have since warned that if the country fails to elect a pro-bailout government sticking to its harsh austerity measures, Athens might have to abandon to euro.
Greece's two biggest parties, the pro-bailout conservative New Democracy and the anti-bailout radical leftist SYRIZA, rejected the idea of a referendum.
"The Greek people don't need a referendum to prove they're pro-euro," said New Democracy leader Antonis Samaras in a statement. "Her idea is unfortunate, to say the least, and can't be accepted," he added.
"Ms. Merkel is used to address Greece's political leaders as if the country was a protectorate," SYRIZA leader Alexis Tsipras said.
Government spokesman Tsiodras said that Greece's current interim government had no authority to call a referendum. "It is obvious that this issue is outside the scope of a caretaker government," he said in his statement.