Mrs Merkel's spokesman yesterday made clear that she viewed the practice, if the reports were correct, as "completely unacceptable" and called for US authorities to clarify the extent of surveillance in Germany.
In a statement, the spokesman said the German government "has received information that the chancellor's cellphone may be monitored by American intelligence".
He would not elaborate but news magazine Der Spiegel, which has published material from NSA leaker Edward Snowden, said its research triggered the response.
The White House said Mr Obama had assured Mrs Merkel that the US was not listening in on her phone calls.
White House spokesman Jay Carney said the two leaders spoke by phone, adding: "The United States is not monitoring and will not monitor the communications of the Chancellor."
Mr Carney said the US was examining Germany's concerns as part of a review of how the US gathers intelligence.
The White House has cited that review in responding to similar spying concerns from France and other US allies.