The package includes $810 million to assist refugees from and people displaced within Syria and Iraq -- triple the amount Japan provided last year, and $750 million for peace building in the Middle East and Africa.
Japan has set aside another $2 million to assist Lebanon, which hosts more than 1.1 million Syrian refugees, and $2.5 million to assist Serbia and Macedonia, through which refugees flee en route to the European Union.
"Each of these assistance measures is an emergency countermeasure that Japan is able to undertake," Abe told the UN General Assembly.
"But at the same time our unchanging principle is at all times to endeavor to return to the root of the problem and improve the situation."
The $750 million set aside for Iraq, and the wider Middle East and North Africa is expected to go on peace and stability efforts such as vocational training, and providing dependable water and sewage facilities.