General Keith Alexander never discussed alleged operations involving Angela Merkel, an NSA spokeswoman said.
German media say the US has been tapping Angela Merkel’s phone since 2002, and Barack Obama was told in 2010.
The row has led to the worst diplomatic crisis between the two countries in living memory.
A report in German tabloid Bild am Sonntag claimed that Gen. Keith Alexander had told Barack Obama about the bugging himself.
An NSA source told the paper that Barack Obama had not stopped the operation, and had wanted to know all about Angela Merkel as “he did not trust her”.
However, a statement from the NSA on Sunday denied the reports in Bild.
“[General] 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,” NSA spokeswoman Vanee Vines said.
“News reports claiming otherwise are not true.”
The statement does not make it clear whether the president was informed of the bugging operation by other means.
Barack Obama is reported to have told the German chancellor that he knew nothing of the operation when the two leaders spoke on Wednesday.
Germany is sending its top intelligence chiefs to Washington in the coming week to “push forward” an investigation into the spying allegations, which have caused outrage in Germany.
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