Authorities in Tamil Nadu state cancelled the group`s registration earlier this month.
India has previously accused the group of having an anti-development agenda.
Greenpeace lawyer Vineet Subramani told the AFP news agency that the judge had observed "prima facie, the government has not followed the principles of natural justice".
The move was the latest in a series of actions aimed at Greenpeace and a number of other organisations whom the authorities have accused of working against the country`s interests.
In April the government suspended Greenpeace`s registration and froze its domestic bank accounts for alleged violations. The group successfully challenged the order in court.
But later Tamil Nadu, where Greenpeace was registered, cancelled the permit.
The group has claimed orders came from the home ministry, but the home ministry had not commented on these claims.
Separately, in September India cancelled a licence allowing Greenpeace`s local unit to receive donations from abroad. The order was also overturned.
Indian Prime Minister Narendra Modi`s government has cancelled the foreign funding licences of around 9,000 charities since a major crackdown began in April, according to AFP.
Greenpeace has been working in India for 14 years and employs more than 300 people.
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