Obama and Merkel exchanged views on US-German intelligence cooperation during their first conversation Tuesday after a new spy row damaged the allies' relations, Xinhua reported.
According to a White House statement, Obama said he would remain in close communication on ways to push cooperation forward.
Germany on Thursday asked the US intelligence chief in Berlin to leave the country as a new round of allegations of US espionage is threatening to strain bilateral ties.
The bilateral ties were damaged by revelations of data gathering practices by former US intelligence contractor Edward Snowden last year.
While talking about bilateral relations, the two leaders also discussed the situation in Ukraine and the ongoing talks on Iran's nuclear program, the statement said.