Trong's trip comes just two months after Dung travelled to Japan and held talks with Abe and is the latest of a series of visits by high-ranking officials from Vietnam.
Having visited Washington and Beijing this year, the 71-year-old leader expressed his desire to come to Japan ahead of a change in the Communist Party leadership early next year.
As Tokyo and Hanoi cement their "extensive strategic partnership," the two countries agreed to cooperate in agriculture, a priority area for Vietnam. According to the statement, Vietnam will open its market to Japanese apples, while Vietnamese mangoes will enter the Japanese market soon.
On a broader scale, the two said they will continue working for the early conclusion of the US-led Trans-Pacific Partnership initiative, the document said.
While Japan has strengthened its economic ties with Vietnam, with government data showing the number of Japanese companies rose to about 1,400 as of this year, China is Vietnam's largest trading partner.