Obama is expected to announce the change at the White House later Friday and will reportedly replace Jones, 66, with his deputy, Tom Donilon.
Jones' departure was expected, as he had apparently indicated to his staff his intention to leave by the end of 2010. His departure follows that of Obama's chief of staff, Rahm Emanuel, who left the White House last week to run for mayor of Chicago.
Recently, the White House staff criticised Jones for comments he apparently made to Bob Woodward, the author of "Obama's Wars", a book that describes deep divisions in the White House over the war in Afghanistan, the Times reported.
Woodward's book portrayed Jones as often being at odds with Obama's political aides, including Emanuel, senior adviser David Axelrod and spokesman Robert Gibbs. According to the book, Jones referred to the group as "water bugs", the "Politburo", or the "Mafia".
Jones is a retired four-star Marine general who made history in January 2003 with his appointment as NATO's supreme allied commander in Europe and head of the US forces on the continent. It marked the first time a Marine was chosen to head the alliance. He had previously served as commandant of the Marine Corps.
He retired in 2007 after 40 years of military service, but still advised the Bush administration on security issues in the Middle East.Jones is a decorated Vietnam War veteran and in 1992 became a deputy director of the US European Command. He later oversaw some missions in Bosnia-Herzegovina and Macedonia.
Jones' departure follows that of Emanuel and the announcement that Obama's top economic adviser, Lawrence Summers, will leave at the end of the year to return to Harvard University.
