Japanese defence has been changing since 2007, and it has undertaken harsh security measures at home and abroad including the reinterpretation of the Clause-9 of its constitution. These defence changes have been negatively impacting upon Japanese policies and ties with the region of North East Asia and South Asia. Japan has been worsening its ties both with China by installing the Terminal High Altitude Area Defense (THAAD), and by a nuclear deal struck with India that would damage its ties with Pakistan in the South Asian regional security perspectives. India is now heavily armed by both Japan and the United States. In a major defence shift, Prime Minister Shinzo Abe lifted a 50-year ban on arms exports. In a recent move, Japan has supplied 12 amphibious rescue aircraft from Japanese manufacturer Shin Maywa Industries worth US$1.5 billion. India would use these aircraft for surveillance purposes in the South China Sea against PLA’s of China and in the Indian Ocean against China and Pakistan to disrupt the China-Pakistan Economic Corridor (CPEC) and peaceful use of Gwadar shipment for commercial purposes. Abe’s change of defence policy in favour of India consequently counters the China-Pakistan all-weather friendship that has been recently reshaping their growing ties in the Indian Ocean after the inauguration of the Gwadar port shipment on 13 November. The India-Japan defence collaboration is just not ended here. Both countries have signed the most controversial and long-pending civil nuclear deal on 11 November. Negotiations for the deal were started in 2010 and a number of round of talks were held. The deal has removed the hurdle in supplying Japanese nuclear power plants and equipment to India to boost its energy. The Indo-Japanese deal would also enable the United States, France, and Australia to supply nuclear materials to an NPT/CTBI handicapped India, giving a heavy blow to the global non-proliferation regime. Pakistan is directly affected by the Indo-Japanese nuclear deals for a variety of reasons. The Indo-Japanese nuclear deal introduced an element of ”nuclear discrimination” by excluding Pakistan and also jointly targeting it. The nuclear deal also changed Japanese foreign policy toward South Asia. It is no longer a silent partner and a balancer in South Asia. It has ended its neutrality in favour of India. Japan’s role has become controversial. For decades, after World War II, Japan strictly maintained its neutrality and became an indispensable economic partner of all South Asian countries. Although India questioned Japan’s military alignment with the United States during the Cold War, it was largely accepted as a development partner of many South Asian countries, and aid and technology provider to them. The Indo-Japanese civil nuclear deal has drastically altered this political and strategic equilibrium. Pakistan is an energy-deficit country. Nuclear power energy is just one percent of its energy mix, and it’s desperately looking to diversify its energy mix by looking at cheaper and economical sources of energy production. Japan disrespects Pakistani viewpoint. Japan’s civil nuclear cooperation with India is pushed by the Indo-American nuclear deal of 2005 and the waiver it extended to India in the NSG in 2008. Japan’s anti-nuclear credentials have also been violated, and Japan has emerged as a source of nuclear materials to India. The entire civil nuclear program of Pakistan has been assisted by China since the 1980s under IAEA’s safeguards and framework. The Indo-Japanese nuclear deal has further pushed Pakistan into China’s hold to accelerate its civil nuclear program. Pakistan’s first nuclear power plant KUNUPP would be decommissioned within the next three years. Three nuclear power plants have been running at Chasma. Two more power plants will be built at the same site and two coastal power projects at Karachi and all with the use of Chinese technology. Japan has the ability to help diversify Pakistan’s nuclear program, but it is reluctant to do so and has a tilted toward India. Pakistan has a better nuclear safety program than India and Japan. Both countries encountered nuclear incidents. The Fukushima meltdown is the most horrible example, but countries like the United States, France, Australia, as well as, Japan discriminate Pakistan in diversifying its civil nuclear program. The Indo-Japanese civil nuclear deal has come against the backdrop of the growing China’s expanding role in the Indian Ocean and South China Sea. The deal aims at curtailing Chinese role and influence in these regions. The peaceful use of nuclear energy by India is also highly doubtful. Statements from New Delhi say that there is no bar on India to conduct tests. Statements from Tokyo negate all such claims and say that India needs written permission from Japan to do so. “There is no effective separation between India’s nuclear energy program and its weapons program, and the Japanese Government’s agreement conditions are meaningless, stated by Shaun Burnie, a senior nuclear specialist at Greenpeace Japan. The women of Fukushima, an anti-nuclear lobbying group, have issued an appeal to the Indian Prime Minister Narendra Modi to visit the Fukushima disaster area and see himself the consequences of a nuclear disaster. Japan, under the hawkish Prime Minister Shinzo Abe, is more interested in commercialising the sale of nuclear power plants to India to boost its exports but this could pose dangerous physical consequences and to alter the existing balance of power in South Asia. The writer is a Senior Research Fellow at the Institute of Strategic Studies Islamabad. He writes on East Asian affairs