The letter from Shinzo Abe to Xi Jinping did not contain any substantial overtures, but it sent wishes of good health, spoke of the two countries' "shared responsibility for peace and prosperity" in the region.
It added that the meeting was a "valuable opportunity to share views".
The meeting between Mr Xi and the envoy, senior lawmaker Natsuo Yamaguchi, appeared to reduce some of the intensity of the dispute, which has raised concerns over a possible armed conflict.
Mr Xi told Mr Yamaguchi that China attached "great importance" to his visit, held in Beijing's Great Hall of the People following four months of rising friction that have included violent protests in China and the scrambling of fighter jets by both countries.
Mr Yamaguchi said both men emphasised the need for discussion and calm.
He said they discussed a future meeting in preparation for a possible summit between Mr Xi and Mr Abe, but gave no indication when that might happen.
Tensions soared after Japan's government bought the uninhabited islands, known in Chinese as Diaoyu and Japanese as Senkaku, from their private Japanese owners in September.