President Barack Obama learned of the electronic surveillance in an internal review he ordered at mid-year, the Journal reported, citing unnamed US officials.
The review showed that the NSA had tapped the phones of some 35 world leaders. The White House ended programs tracking several of the leaders including Merkel, according to the Journal.
Some programs have been scheduled to end but have not yet been terminated, the Journal said.
Officials told the Journal that there are so many NSA eavesdropping operations that it would not have been practical to brief the president on all of them.
Obama was "briefed on and approved of broader intelligence-collection 'priorities,'" but deputies decided on specific intelligence targets, the Journal said.
"These decisions are made at NSA," the unnamed official told the Journal. "The president doesn't sign off on this stuff."
Ending a surveillance program is complicated because a world leader like Merkel may be communicating with another leader that Washington is monitoring, officials told the newspaper.
Germany's Bild am Sonntag weekly quoted US intelligence sources on Sunday as saying that NSA chief General Keith Alexander briefed Obama on the operation against Merkel in 2010.
In Washington, NSA spokeswoman Vanee Vines denied the claim.
Alexander "did not discuss with President Obama in 2010 an alleged foreign intelligence operation involving German Chancellor Merkel, nor has he ever discussed alleged operations involving Chancellor Merkel," Vines said.
"News reports claiming otherwise are not true," she said.
The snooping allegations, based on documents leaked by fugitive former US defense contractor Edward Snowden, indicate that US spy agencies accessed the electronic communications of dozens of world leaders and likely millions of foreign nationals.