Meiji period
Environmental pollution has accompanied industrialization since the Meiji period. One of the earliest cases was the copper poisoning caused by drainage from the Ashio Copper Mine in Tochigi prefecture, beginning as early as 1878. Repeated floods occurred in the Watarase river basin, and 1,600 hectares of farmland and towns and villages in Tochigi and Gunma prefectures were damaged by the floodwater, which contained excessive inorganic copper compounds from the Ashio mine. The local farmers lead by Shozo Tanaka, a member of the Lower House from Tochigi appealed to the prefecture and the government to call a halt to the mining operations. Although the mining company paid compensatory money and the government engaged in the embankment works of the Watarase river, no fundamental solution of the problem was achieved. The pollution had decreased since the early 20th centurys.

?Environment deterioration in 1960s
Main article: Four Big Pollution Diseases of Japan
Current Japanese environmental policy and regulations were the consequence of a number of environmental disasters in 1950s and 1960s. Cadmium poisoning from industrial waste in Toyama Prefecture was discovered to be the cause of the extremely painful itai-itai disease (???????, Itai itai by??, lit. "ouch ouch sickness") which causes severe pain in the back and joints, contributes to brittle bones that fracture easily, and degeneration of the kidneys. Recovery of cadmium effluent halted the spread of the disease, and no new cases have been recorded since 1946. In the 1960s, thousands of inhabitants of Minamata City in Kumamoto Prefecture were poisoned by methyl mercury drained from the chemical factory, known as the Minamata disease. The number of casualties in Minamata is 6,500 as of November 2006. In Yokkaichi, a port in Mie Prefecture, air pollution caused by sulfur dioxide and nitrogen dioxide emissions led to a rapid increase in the number of people suffering from asthma and bronchitis. In urban areas photochemical smog from automotive and industrial exhaust fumes also caused the rise in respiratory problems. In the early 1970s, chronic arsenic poisoning attributed to dust from arsenic mines occurred in Shimane and Miyazaki prefectures.

Today
In the 1990s, Japan's environmental legislation was further tightened. In 1993 the government reorganized the environment law system and legislated the Basic Environment Law (?????) and related laws. The law includes restriction of industrial emissions, restriction of products, restriction of wastes, improvement of energy conservation, promotion of recycling, restriction of land utilization, arrangement of environmental pollution control programs, relief of victims and provision for sanctions. The Environment Agency was promoted to full-fledged Ministry of the Environment in 2001, to deal with the deteriorating international environmental problems

In a 1984 the Environmental Agency had issued its first white paper. In the 1989 study, citizens thought environmental problems had improved compared with the past, nearly 41 % thought things had improved, 31 % thought that they had stayed the same, and nearly 21 % thought that they had worsened. Some 75 % of those surveyed expressed concern about endangered species, shrinkage of rain forests, expansion of deserts, destruction of the ozone layer, acid rain, and increased water and air pollution in developing countries. Most believed that Japan, alone or in cooperation with other industrialized countries, had the responsibility to solve environmental problems. In the 2007 opinion poll, 31.8% of the people answered environmental conservation activity leads to more economic development, 22.0% answered the environmental activity does not always obstruct the economic, 23.3% answered environmental conservation should be given preference even if it may obstruct the economic and 3.2? answered economic development should place priority than environmental conservation.

The OECD's first Environmental Performance Review of Japan was published in 1994, which applauded the nation for decoupling its economic development from air pollution, as the nation's air quality improved while the economy thrived. However, it received poorer marks for water quality, as its rivers, lakes and coastal waters did not meet quality standards. Another report in 2002 said that the mix of instruments used to implement environmental policy is highly effective and regulations are strict, well enforced and based on strong monitoring capacities.

In the 2006 environment annual report, the Ministry of Environment reported that current major issues are global warming and preservation of the ozone layer, conservation of the atmospheric environment, water and soil, waste management and recycling, measures for chemical substances, conservation of the natural environment and the participation in the international cooperation.