The agreement was reached when Japanese Prime Minister Yoshihiko Noda met with his Mongolian counterpart Sukhbaatar Batbold, who began a six-day visit to Japan on Saturday, the officials said.
The two leaders also agreed their two countries would promote cooperation in the development of natural resources and infrastructure, according to a joint announcement released after the meeting.
Mongolia is rich in resources including coal, copper, gold, uranium and rare metals.
Batbold told Noda he would welcome Japanese investment, especially in the development of infrastructure in the massive Tavan Tolgoi coal mine, the officials said.
The two leaders also signed a document in which Japan pledged to extend a low-interest government loan worth 1.55 billion yen ($19 million) to help Mongolia's poor with health and medical support.
Japan will also provide Mongolia with three grants worth abut 1.2 billion yen.
Mongolia, whose economy grew by 17.3 percent in 2011, has no free trade accords with other countries.
Japan's exports to Mongolia totalled about 13.8 billion yen in 2010 when the reverse flow of merchandise came to only 1.6 billion yen.