Some of the victims jumped from third-story windows to escape the fire. Three people remained hospitalized, said Tokyo Fire Department spokesman Takashi Yamagishi.
"I saw a man jump off the building and thought it was a suicide. Then I saw smoke pouring out of the building," a man in his 20s told local television.
Television footage showed firefighters scrambling up ladders to reach the third and fourth floors of the building in the Kabukicho entertainment district, which were gutted by the blaze.
Police at first said that 47 people were hospitalized with injuries, but Yamagishi later said 44 were killed and three who were injured remained hospitalized. Their conditions were unknown.
The fire was extinguished and a search by rescuers showed that there were no more victims, according to Japanese public broadcaster NHK television.
It was unclear how many people were inside the mahjong parlor where the blast occurred, on the third floor of the four-story building. Some people scampered to the roof and were rescued.
Officials were trying to determine the cause of the explosion and fire, said a spokesman at the Shinjuku police station who gave only his last name, Masuda.
News reports said the explosion occurred when an employee of the mahjong parlor opened the door of the establishment. Mahjong is a popular table game in much of East Asia and sometimes involves gambling.
Kyodo News agency said the building included a number of entertainment shops, including restaurants and sex establishments. It said the blast tore a hole large hole in the side of the building.
Kabukicho is one of Tokyo's busiest nightclub areas and is not far from the city's most crowded train station.
The number of casualties was the highest in Japan since 1982, when 33 people were killed and 29 others injured in a fire that gutted a hotel in the Akasaka area of central Tokyo.
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