In total the ministry said 54 people have died in Japan while taking the drug, but it said while there were concerns about psychiatric problems there was no direct proof of a link between Tamiflu and abnormal behaviour.
Japan buys more than 60 per cent of the world's Tamiflu supply, also known as oseltamivir.
Although it is seen as the frontline drug against a global bird flu pandemic, Tamiflu is also used in many cases to treat normal flu.
The new warning, carried by Japanese Tamiflu distributor Chugaui Pharmaceuticals, is to include the words: "Except in cases judged to be high risk, avoid prescribing this drug to minors over the age of 10."
'No causal link'
On Tuesday the Swiss-based manufacturer of Tamiflu, Roche Holding AG, said data from Japan and the US showed no causal link between the drug and neuropsychiatric symptoms. '
It has denied any link between the drug and abnormal behaviour among young people although the drug already carries warnings in Japan and the US about such side effects.
A spokesman for Chugai said Roche has been advised of the warning.
"Since patients taking Tamiflu have exhibited abnormal behaviour and fallen from buildings, we must accept this procedure.
"We want to raise awareness as quickly as possible," he added.
More than 100 cases of delirium, hallunications and other unusual psychiatric behaviour, mostly in Japanese children taking Tamiflu, were reported between August 2005 and July 2006, according to the US Food and Drug Administration.
The Japanese government has yet to release the detailed figures of the study.
The virulent H5N1 bird flu virus has killed around 160 people across the world since late 2003, mostly through contact with infected birds.
Health officials have warned that it could mutate into a form easily transferable between humans, sparking a global pandemic.
Last week however Japan declared an end to its outbreaks of the virus.