The offer was announced Friday after Japanese Foreign Minister Fumio Kishida visited his Vietnamese counterpart, Pham Binh Minh in Hanoi, Vietnam.
The six used boats, with training and coast-guarding surveillance equipment, are valued at $5 million.
Kishida said Vietnam and Japan support "maintaining peace and stability" in the contested region.
Japan and China each claim islands called Diaoyu in Chinese, or Senkaku in Japanese. Taiwan, China and Vietnam each claim a string of islands called Xisha in Chinese or the Hoang Sa archipelago in Vietnamese -- islands also known as the Paracel Islands.
Chinese and Vietnamese ships clashed in May in the area after China moved an oil rig into waters off Vietnam's coast, causing anti-Chinese rioting in Vietnam in which at least two people died and several factories were burned.
The Japanese gift of the boats could be interpreted as a sign of Japanese solidarity with Vietnam, against China.