In a rare defeat for the Japanese government in its own courts, fishermen Monday won an order keeping the gates of a sea dyke open, despite authorities saying it was a defence against flooding.

Japanese governments have for decades invested heavily in public works projects, concreting hillsides, riverbanks and coastlines, in projects that have often been criticised as environmentally damaging pork-barrel exercises.

Among them is the dyke at Isahaya Bay in Nagasaki Prefecture.

Japan's central government first planned the seven-kilometre (4.3-mile) sea dyke in the 1950s to reclaim a coastal wetland for rice cultivation, and later argued that it also served as a protective barrier against floods.

But environmentalists say that enclosing the wetland, a key habitat for migratory birds, damages it.

Similarly, commercial fishermen who trawl the bay outside the wetland argue that it provides important nutrients for ocean marine life such as seaweed as its mud is flushed into the sea with the daily ebb and flow of the tide.

Over the years fishermen staged sit-ins to try to prevent the dyke's construction, and in a 2008 district court ruling the government was ordered to keep open two of the dyke's drainage gates for five years.

On Monday the Fukuoka High Court upheld the decision, in the latest stage of the long-running battle.

Presiding Judge Hiroshi Koga said: "It is illegal for the state to infringe upon the fishing rights by keeping the gates shut," Japanese media reported.

"While the plaintiffs' fishing rights are greatly violated, the effect of the sea dyke against disasters is limited."

Outside the court supporters rejoiced, punched the air with their fists and shouted "banzai" (hurrah!), holding up banners reading "Victory in court" and "The agriculture and fisheries ministry condemned again".

The centre-left Democratic Party government that took power over a year ago has decried the public works habit that has also seen hundreds of dams and so-called bridges to nowhere built, pledging instead to put "people before concrete".