In a 40-minute phone call Wednesday morning Japanese time, Obama expressed regret to Abe (pictured above) over the allegations.
"President Obama said he was very sorry... as the case caused a big debate in Japan," Japanese Chief Cabinet Secretary Yoshihide Suga said without confirming the spying claims.
Suga added that Abe told Obama that if the allegations were true, "it could shake our relationship of trust."
In July, WikiLeaks posted online what appeared to be five U.S. National Security Agency (NSA) reports on Japanese positions on international trade and climate change.
The reports were allegedly gleaned from intercepts from 2007 to 2009, revealing years-long espionage on Japanese officials and major companies.
WikiLeaks also posted what it says was an NSA list of 35 top surveillance targets in Japan, including the Cabinet Office, the finance and trade ministries and prominent Japanese companies.
Japan's 'muted' response over spying claims
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 seen as one of Washington's key allies in the Asia-Pacific region and they regularly consult on defense, economic and trade issues.
Unlike German Chancellor Angela Merkel and French President Francois Hollande, Abe did not appear to be a direct target of wiretapping, although other senior politicians allegedly were, including Trade Minister Yoichi Miyazawa.
WikiLeaks claims of widespread NSA spying in Germany
According to documents leaked by whistleblower Edward Snowden in 2013, the NSA tapped Merkel's mobile phone. But in June, Germany's Federal Prosecutor's Office closed its investigation into the alleged tapping after saying that the leaked documents did not contain evidence of surveillance.
A more recent batch of documents released by WikiLeaks in July suggested that NSA spying on German officials was even more widespread and went on for far longer than previously thought.
Wikileaks claimed that a list of 56 partially-redacted phone numbers it published in July showed that the NSA targeted officials including both former German Chancellor Gerhard Schröder and his predecessor, Helmut Kohl.
Also on the list were numbers attributed to former diplomat Geza Andreas von Geyr, who now works for the Ministry of Defense, and Ronald Pofalla, who was the former head of Angela Merkel's chancellery between 2009 and 2013.
The July disclosures came barely a week after WikiLeaks posted documents from the 1990s revealing contact details of various officials in Germany's Finance Ministry, as well as staff in the Ministry of Agriculture, European policy advisers and an official working in the European Central Bank.
France has also recently been hit by NSA-spying revelations dating between 2006 and 2012 - impacting on Presidents Jacques Chirac, Nicolas Sarkozy and Francois Hollande.
mh/msh (AFP, AP, dpa)