"We looked forward to your visit which would open up a new page in the history of Japan-China military exchange," he said.
The port call is part of a planned series of exchanges that will see Japan sending a warship on a similar visit to China at a later date.
Cui Tiankai, China's ambassador to Japan, said the warship was a "messenger of peace and friendship" which aims to relay "the hope for a harmonious Asia and a harmonious world".
|The Shenzhen will be open to visitors during |
its four day stay in Tokyo [Reuters]
"Japan and Chinese relations are at an important point," he said.
"China is following the path of peace and partnership, and Japan is an important neighbour for China."
Before the Shenzhen's trip to Japan, Beijing expressed hope that the visit would "have a positive effect on the development of the relationship between the two countries and their defence departments".
The two countries had in 2000 agreed to reciprocal naval visits but China cancelled a planned port call two years later after Japanese leaders visited a controversial Tokyo shrine, seen in China as a symbol of Japan's past militarism.
Diplomatic relations between the two economic and political rivals have visibly improved over the past year.
The Chinese warship arrived under heavy escort, greeted by hundreds of flag-waving Chinese residents in Japan and a lion dance performance while a navy band on board played "Anchors Away".
The vessel will be open to the public during its four-day stay in Tokyo, providing visitors a rare glimpse of its high-tech weaponry.
Relations between China and Japan have eased markedly in recent months, but several issues remain unresolved:
|Disputed territory is just one of |
many unresolved issues [EPA]
War shrine visits
China frequently protests against Japanese political leaders visits to Tokyo's Yasukuni shrine - particularly visits coinciding with the anniversary of Japan's Second World War surrender. It argues the shrine honours several convicted war criminals and shows Japan has not atoned for its past war crimes.
China and Japan both lay claim to the uninhabited Diaoyu/Senkaku islands, located between Taiwan and Okinawa. The islands are thought to lie near major oil and gas reserves.
Controversial revisions to Japanese history textbooks - amending or removing references to wartime atrocities committed by the Japanese military - frequently draws criticism from China. A particular focus of dispute has been over the 1937 "Rape of Nanjing" in which up to 300,000 Chinese civilians were killed by occupying Japanese forces.