Government health chiefs claim a four-year experiment with it has had serious financial and human costs.
Of the 3,969 medical compensation claims relating to vaccines in the last 30 years, a quarter had been made by those badly affected by the combined measles, mumps and rubella vaccine, they say.
The triple jab was banned in Japan in 1993 after 1.8 million children had been given two types of MMR and a record number developed non-viral meningitis and other adverse reactions.
Official figures show there were three deaths while eight children were left with permanent handicaps ranging from damaged hearing and blindness to loss of control of limbs.
The government reconsidered using MMR in 1999 but decided it was safer to keep the ban and continue using individual vaccines for measles, mumps and rubella.
The British Department of Health said Japan had used a type of MMR which included a strain of mumps vaccine that had particular problems and was discontinued in the UK because of safety concerns.
The Japanese government realised there was a problem with MMR soon after its introduction in April 1989 when vaccination was compulsory. Parents who refused had to pay a small fine.
An analysis of vaccinations over a three-month period showed one in every 900 children was experiencing problems. This was over 2,000 times higher than the expected rate of one child in every 100,000 to 200,000.
The ministry switched to another MMR vaccine in October 1991 but the incidence was still high with one in 1,755 children affected. No separate record has been kept of claims involving autism.
Tests on the spinal fluid of 125 children affected were carried out to see if the vaccine had got into the children’s nervous systems. They found one confirmed case and two further suspected cases.
In 1993, after a public outcry fuelled by worries over the flu vaccine, the government dropped the requirement for children to be vaccinated against measles or rubella.
Dr Hiroki Nakatani, director of the Infectious Disease Division at Japan’s Ministry of Health and Welfare said that giving individual vaccines cost twice as much as MMR ‘but we believe it is worth it’.
In some areas parents have to pay, while in others health authorities foot the bill.
However, he admitted the MMR scare has left its mark. With vaccination rates low, there have been measles outbreaks which have claimed 94 lives in the last five years