The violence came days after the mayor of Nagasaki was gunned down by a reputed mobster in an unrelated killing. Crime syndicates are overwhelmingly responsible for Japan's rare gun attacks.
The events began Friday when the suspected gangster allegedly shot and killed another mobster from the same group on the street in a western suburb of Tokyo, police said.
The shooter, identified as 36-year-old Yuji Takeshita, then barricaded himself inside his own apartment, firing a series of shots at surrounding officers, said a Tokyo Metropolitan Police spokesman who spoke on condition of anonymity, under police protocol.
Police threw smoke bombs and stormed the apartment, after which public broadcaster NHK showed paramedics carrying the suspect out on a stretcher. The police spokesman said Takeshita is believed to have shot himself in the head and was taken to a nearby hospital. Another official, also speaking on condition of anonymity, said Takeshita was still undergoing treatment early Saturday afternoon.
Investigators later found a pair of handguns in his apartment and later arrested him at the hospital for allegedly violating the gun control law, Tokyo police said.
"The cases must be investigated inside out, and I would like (the authorities) to step up anti-crime measures," Prime Minister Shinzo Abe told reporters late Friday. "We must make utmost effort to eradicate such shootings and gangster groups."
On Tuesday a gangster who unsuccessfully sought compensation from the city for damage to his car fatally shot the mayor of Nagasaki. Police arrested Tetsuya Shiroo, a senior member of Japan's largest crime syndicate, the Yamaguchi-gumi, and said he admitted to the attack.
Analysts say the recent shootings are signs that gangsters are getting desperate in keeping their turf and finding income sources since the government stepped up anti-gang measures in the 1990s.
"Gangsters used to keep their guns to themselves, largely to protect their turf," former National Police Agency official Yutaka Takehana told public broadcaster NHK. "The recent cases indicate gang groups are getting desperate for money."
Shiroo's Yamaguchi-gumi branch reportedly had been under financial pressure as it was being outperformed by rival groups, according to Kyodo News agency. Problems a company Shiroo was involved with had obtaining loans from the city may have also accented that pressure and been a motivating factor in the attack, Kyodo said.
Police believe internecine strife has also been generated by the Yamaguchi-gumi's rapid expansion of operations in Tokyo, the traditional base of Japan's second largest gang, the Sumiyoshi-kai.
In a widely publicized turf war that ended a yearlong lull in underworld violence, the boss of a gang affiliated with the Sumiyoshi-kai was shot to death in February. The killing was believed to have prompted at least three more shootings at gangland headquarters in Tokyo.
The high-profile violence alarmed residents of Tokyo and police moved quickly to quell it, raiding the affiliate gang's offices shortly after the attacks.
Handguns are strictly banned in Japan, and only police officers and others -- such as shooting instructors -- with job-related reasons can own them. Hunting rifles are also strictly licensed and regulated.
Crime syndicates, however, have smuggled foreign guns into Japan. Of the 53 shootings reported in 2006, two-thirds -- 36 -- were blamed on organized crime groups, the National Police Agency says.
"If we do not rethink the regulation of gangs and weapons from the bottom up, these horrors are sure to happen again," local daily Tokyo Shimbun said in an editorial Saturday.
Japan's organized crime groups are typically involved in real estate and construction kickback schemes, extortion, gambling, the sex industry and drug trafficking.
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