The publishers put a warning on the cover that the book was not suitable for children and teenagers.
The Complete Manual of Suicide, which has sold 1.2m copies since it was published six years ago, details 10 different ways to die.
Youth suicides in Tokyo rose by 85% last year, and the national rate of all suicides rose by 35%.
Japan has one of the highest rates in the world. Record unemployment, intense exam pressure and an ageing population are thought to be the main causes.
But the book has been linked to the record 74 corpses found last year in Aokigahara - a wood at the foot of Mount Fuji recommended in the manual as "the perfect place to die".
And copies were found beside two young suicide victims in the capital this year, prompting police to demand that sales be limited to people over 18.
The publishers put a warning on the cover that the book was not suitable for children and teenagers.
But the author, Turumi Wataru, told the UK's Guardian newspaper that he wanted under-18s to read the book.
"They need it more than anyone. It is important that people realise that suicide is not wrong. It is the right of every individual to kill themselves and, no matter what laws you enact, you cannot stop it."
The Japanese have long regarded suicide as an honourable way to atone for failure and express remorse.
New regulations
Under existing bylaws, the Tokyo metropolitan government can only prohibit the sale of publications with sexual or violent content.
But officials are considering new regulations, which, if approved, could be in place by the end of 2000.
Suicide prevention groups told the newspaper that action was necessary.
"We have had calls from people in great pain because they followed the book's instructions, but failed to kill themselves," Yukiko Nishihara, founder of a Tokyo helpline said.
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