Oil fuels Asian giants' tensions
Tokyo says Beijing has now expressed regret over the incident, after finally acknowledging that the submarine in question was indeed Chinese.
Both sides are hoping the submarine incident can now be put behind them.
But it will have done nothing to reassure either about the other's intentions.
After years of economic and political stagnation, Japan has been deeply alarmed by China's rapid rise. Its initial response, after the submarine was spotted last week, may have reflected a new, tougher line towards its giant neighbour.
Despite the constraints of its pacifist constitution, Japan scrambled a military aircraft and chased the submarine with destroyers, before accusing China of violating its sovereign rights and demanding a formal apology.
Beijing's ambassador to Japan, without acknowledging Chinese involvement in the incident, called at the weekend for the two countries to work towards improving relations.
But he did not miss the opportunity to restate China's displeasure at Japanese Prime Minister Junichiro Koizumi's repeated visits to Tokyo's Yasukuni Shrine.
The controversial shrine is dedicated to Japan's war dead, including war criminals, and also including those who took part in Japan's brutal occupation of northern China from 1931-45.
Ren Xiao of the Shanghai Institute for International Studies told BBC News that many Chinese have a "victim complex" and it is hard for them to forget about history.
Japan is partly to be blamed for this, he added.
"(Chinese people) are sceptical of what Japan has been doing these days, including sending more peacekeeping troops abroad, dispatching troops to Iraq, and the possible amendment to their constitution," said Mr Ren.
These fears have been fanned because Tokyo and Washington have been discussing an expanded role for Japanese forces within the US-Japan Defence Treaty - a move China believes is aimed at containing its growing power.
Japan also wants to become a permanent member of the UN Security Council. Again, China - already a permanent member - makes little secret of its opposition.
Battle for resources
As well as the tensions resulting from their troubled history, Shen Dingli, an international relations specialist at China's Fudan University, points to two contemporary problems.
First, he said that "Japan has joined the US in a military alliance that deters China's efforts in unifying with Taiwan." And second, the two countries are competitors for oil resources.
A recent discussion paper prepared for Japan's Defence Agency reportedly warned that either of these issues could trigger a Chinese military attack on Japan.
The discussion paper was dismissed by China as evidence of Japan's "Cold War thinking".
But it did highlight the potential for further tensions, specifically over a group of disputed islands, known as Senkaku in Japan and Diaoyu in China, and Chinese gas field explorations in areas Japan regards as its exclusive economic zone.
Given that both countries are highly dependent on oil imports to fuel their huge economies, it is the energy issue that is now at the forefront of their rivalry.
They have been competing for some time over whether an oil pipeline to be developed from Russia should end in Japan or China.
And only last week, China said that Iran wanted it to replace Japan as the Middle Eastern nation's top oil buyer.
It is a critical situation, according to Kyoshi Mori of the Japanese External Trade Organisation.
But he believes the two countries' common position as energy importers could be turned to their mutual advantage if they would only agree to work together.
"In the longer term it can be a win-win situation. It is time for us to unite as one," Mr Mori told BBC News.
"If we act separately it is good only for the suppliers".
A recent issue of the Beijing Review took a similar line, saying energy supply was the very area in which China and Japan could start to co-operate.
"Maybe the energy issue will serve as a turning point of China-Japan relations and even the turning point of East Asia co-operation", said the state-run Chinese magazine.
After all, economic ties are already strong. Many Japanese firms have moved their factories to the Chinese mainland. And for the first time, Japan now sells more to China than to the US.
Some observers believe the two Asian countries may in fact be much closer on many fronts than their war of words suggests.
Robert Sutter, a former member of the US Government's National Intelligence Council, said that the recurring tensions between China and Japan remain serious.
But Mr Sutter, now with the School of Foreign Service at Georgetown University, did not believe the two Asian powers were heading towards military conflict.
"The tensions remain held in check by both governments' strong focus on domestic nation building, their increasingly interdependent economies, and by the fact that no other nation in the region, including the United States, favours a serious worsening of China-Japan relations," he said.