The move comes in response to an alleged serial murder case in which such sites were used.
In October, nine dismembered bodies were discovered in coolers and tool boxes in a so-called "house of horrors" in the suburbs of Tokyo.
Investigators found nine heads along with a large number of arm and leg bones.
Takahiro Shiraishi, 27, has admitted to killing nine people since late August in a case that has stunned Japan.
How did he find his victims?
Police say Mr Shiraishi came to know his victims through social media, where they had expressed suicidal thoughts.
It is alleged that he killed them after luring them to his apartment, saying he would help them take their own lives.
Mr Shiraishi's nine victims included three high school students - the youngest aged 15 - a female student, four women in their twenties and a 20-year-old man.
The only male in the group was killed after confronting Mr Shiraishi about the whereabouts of his girlfriend, Japanese media reported.
Nine bodies were found at the suspect's flat
The discovery at his flat was made as police were looking into the disappearance of a young woman.
Police say she had gone on social media looking for somebody to take her life with.
What are suicide websites?
Suicide websites and social media groups can provide information to individuals who wish to kill themselves.
Such sites can promote and encourage others to take their own lives.
Toru Igawa, the head of a Tokyo-based suicide prevention centre, told the Japan Times that the internet can make things worse for young Japanese people.
He says that previously some people had baulked at killing themselves because they had not wanted to die alone - but suicide platforms and social media have changed that.
"It may now be easier to overcome that hurdle after finding online companions," he said.
A 2015 UK study found that 20% of young adults with a history of suicidal self-harm had visited sites containing information on how to kill or hurt oneself, compared with just three percent of young adults more broadly.
What can the Japanese government do?
A senior member of the government - the Chief Cabinet Secretary, Yoshihide Suga - has instructed ministers to step up measures against so-called "suicide websites" and social media.
"The use of Twitter - a social networking site that is difficult to keep an eye on - to exploit the cries for help by victims who wrote about committing suicide is despicable," he said.
"We will get to the bottom of this crime, and work towards preventing its re-occurrence."
Mr Suga has asked ministers to study the spread of suicide websites and to cooperate with web operators and the authorities.
Japan has a relatively high suicide rate
He asked them to step up measures to delete or restrain problematic sites.
The Japanese authorities have sought to tackle the issue for a long time.
Since the first reported internet suicide pact in 2003, the government has taken action to try to cut the country's high suicide rate through counselling programmes and blocking websites that offer suicide tips.
How high are suicide rates in Japan?
According to World Health Organization statistics, 19.7 per 100,000 people took their own lives in 2015.
Those figures do not make Japan's the highest suicide rate in the world in a developed nation.
In South Korea, 28.3 per 100,000 people took their lives in 2015.
In the United Kingdom and United States, this figure was 8.5 and 14.3 per 100,000 people respectively.