Under such circumstances, the official has said, various parties should respect such aspects and any third party should not be involved in our efforts to resolve the disputes.
Hua said the boundary between India and China was yet to be delimited: "There are disputes over the eastern section of the China-India boundary".
However, one global issue was not discussed, namely the disputed South China Sea, in contrast to the previous two India-Japan summits where the summit declarations specifically referred to the South China Sea and reaffirmed the commitment to freedom of navigation and overflight.
"We are now trying to seek a solution through negotiations that is acceptable to both sides".
The foreign ministry's reaction comes as Japanese prime minister Shinzo Abe is visiting India on Wednesday for two days, during which he will hold annual summit talks with Prime Minister Narendra Modi and both will lay the foundation stone of the ambitious Rs 1.08 lakh crore Ahmedabad-Mumbai bullet train project.
He said that development of infrastructure in the northeastern region would help India open out much more to Myanmar, Bangladesh and beyond.
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The incident comes days after a bomb was detonated on a District Line Tube train at Parsons Green station in West London. Anderson told CNN they had no new updates from officials and passengers are re-boarding the aircraft.
About the India-Japan joint statement, Hua said, "The statement mentioned resolving disputes through negotiation and dialogue".
In the past, the Modi government has issued direct mentions of the South China Sea dispute in its past joint declarations, specifically with the United States in 2014, under the presidency of Barack Obama.
The joint statement also said India and Japan are committed to freedom of navigation and the United Nations Convention on the Law of the Sea (UNCLOS) in the Indo-Pacific region, though it did not include a reference to the dispute in the South China Sea. The joint statement issued by the two countries did not specifically mention Arunachal Pradesh, parts of which are claimed by China.
Addressing the media persons here, Shah affirmed that "it is our sovereign right to develop the country inside our boundaries and we will utilise that right".
India and Japan have agreed to enhance defense ties in what is being seen as a clear cut message to China. There are three areas where there is a convergence of interest between India and Japan so as to counter China is - South China Sea, Indian Ocean, and South East Asia. "We hope the normal development of the relationship can be conducive to regional, peace and development and play a constructive role in this process", the Chinese spokesperson added.