"President Obama said he was very sorry ... as the case caused a big debate in Japan," spokesman Yoshihide Suga told a regular news conference, without confirming the spying claims.
"Prime minister Abe told [Obama] that, if the Japanese people concerned were subject to these activities, it would risk jeopardizing trusting relations between allies."
Suga added Abe reiterated his "serious concern" over the case.
The two leaders held the telephone conversation on Wednesday morning, Suga said, adding the pair agreed to work together on global economic issues in the wake of a stock market meltdown sparked by fears over China.
In an earlier conversation with US vice president Joe Biden, Abe voiced similar concerns if the spying claims were confirmed.
Last month, the whistle-blowing website WikiLeaks said it had intercepts revealing years-long espionage by the US 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.
Japan is one of Washington's key allies in the Asia Pacific region and they regularly consult on defense, economic and trade issues.