The Algerian-French husband and his Japanese wife, both Muslims in their 20s, had told Japanese officials they wanted to travel to the region to engage in "humanitarian assistance" but denied they would take part in any fighting.
Officials from both the Japanese and French governments who initially obtained details about the plan from Japanese security authorities tried in vain to persuade the couple not to travel to the region, said a source familiar with the situation.
In early November the couple left Japan and entered Turkey before going to a town near the border with Syria. Their movements since then are unknown.
Tokyo is trying to trace their whereabouts, including the possibility that the couple crossed into areas controlled by IS which holds swathes of Iraq and Syria.
Yesterday the Syrian Observatory for Human Rights claimed that members of the militant group have murdered nearly 2,000 people in Syria since June.
The jihadist group often records killings on video and posts footage on the Internet, a tactic which experts say is meant to sow fear among civilians and rival groups, as well as to attract new recruits.