"President Obama said he was very sorry… as the case caused a big debate in Japan," Suga told a regular news conference, without confirming the spying claims.
Obama held a telephone conversation with Prime Minister Shinzo Abe Wednesday morning, Suga said, adding that the pair agreed to work together on global economic issues in the wake of a stock market meltdown sparked by fears over China.
He added that Abe reiterated his "serious concern" over the case.
"Prime Minister Abe told Obama that, if the Japanese people concerned were subject to these activities, it would risk jeopardising trusting relations between allies," Suga said.
In an earlier conversation with U.S. Vice President Joe Biden, Abe voiced similar concerns if the spying claims were confirmed.
Last month, WikiLeaks said it had intercepts revealing years-long espionage by the U.S. National Security Agency (NSA) on Japanese officials and major companies.
Tokyo’s response has been widely seen as muted compared to the anger expressed in France and Germany following similar NSA spying allegations.