In the latest flare-up with a European ally, the German Government said it had received information that the National Security Agency had targeted Merkel's personal mobile over a series of years in an effort to gain diplomatic intelligence.
Steffen Seibert, a spokesman for Merkel, said the spying "would be a serious breach of trust".
The call to Obama appeared to have been prompted by information from Der Spiegel, a magazine that has begun publishing information from Snowden's trove of stolen classified US files. Der Spiegel reportedly approached authorities with a US document that contained Merkel's mobile phone number, triggering the sharp German response.
"Today President Obama and Chancellor Merkel spoke by telephone regarding the allegations that the US National Security Agency intercepted the communications of the German Chancellor," said White House press secretary Jay Carney. "I can tell you that the President assured the Chancellor that the US is not monitoring and will not monitor the communications of the Chancellor."
He did not rule out the possibility that the US had in the past monitored her telephone, a nuance that was picked up by German diplomats.
Last month, Dilma Rousseff, the Brazilian President, postponed a state visit to Washington in protest at claims the US was intensely spying on her country. Globo TV reported that the NSA targeted Rousseff's aides, collected billions of Brazilian emails and hacked the internal network of Petrobras, the state-run oil company.Telegraph Group Ltd