Obama told Prime Minister Shinzo Abe that he thought the trouble the revelations caused Abe and his government was regrettable, a Japanese government spokesman told reporters.
The 40-minute call took place today morning Japan time.
Japanese officials faced questioning from the media and in parliament after WikiLeaks posted online what appeared to be five US National Security Agency reports on Japanese positions on international trade and climate change. They date from 2007 to 2009. WikiLeaks also posted what it says was an NSA list of 35 Japanese targets for telephone intercepts.
The comments from both sides seemed to echo the exchange between Abe and US Vice President Joe Biden in a similar call earlier this month.
The two leaders also discussed the global economic turmoil, North Korea and climate change.