Humane Society International-India said that it had campaigned to end the "cruel and obsolete" animal testing and had made a series of representations.
It said that the notification dated November 4 recommends the use of OECD (Organisation for Economic Cooperation and Development) validated non-animal alternatives.
"This is a historic decision by the health ministry. Thousands of rabbits will now be spared from one of the most cruel and infamous experiments on rabbits known to mankind.
"We laud the Health Ministry for acting swiftly to notify the rule change and hope that the companies follow this in letter and spirit," said Alokparna Sengupta, Deputy Director of HSI-India.
The Draize test was developed more than 70 years ago to measure eye and skin irritation using rabbits, who are locked in restraints while a test chemical is applied to one eye or to the shaved skin on their backs.
Animals are monitored for up to two weeks, without pain relief, for signs of chemical damage, which can include swelling, ulceration, bleeding and blindness.
"The words and brackets 'the initial toxicity study shall be carried out by non-animal alternative tests as given in Organisation for Economic Cooperation and Development Guidelines, shall be substituted."
The body claimed that the move comes after Union Minister of Women and Child Development Maneka Gandhi wrote to the Ministry regarding the practice, followed by representations from HSI/India.
India has been a full adherent to the Organization for Economic Cooperation and Development decision regarding Mutual Acceptance of Data since 2011.
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