It said the talks made "particular reference to initiatives aimed at promoting peace and stability in the Asian continent" and Abe thanked Francis for his support in the wake of the devastating earthquake and tsunami in Japan.
East Asia is riven with tensions from the Korean peninsula to the large number of small islands claimed by China.
Francis will travel to South Korea on August 13-18.
Abe and Francis also talked about "Japan's commitment to cooperation for development, especially in Africa, attention to the environment, and nuclear disarmament".
Japanese Catholics are now estimated to number around 440,000 out of a population of some 127 million people.