Husain has over 95 cases registered against him in different parts of the country for his paintings of goddesses that some Hindus find sacrilegious.
Dismissing the PIL, Chief Justice KG Balakrishnan said, "Can't do anything about these individual complaints."
The Chief Justice pointed out that all the cases against the artist have earlier been transferred to Delhi.
The petition also requested that conditions should be made conducive for him to come back to India
Husain, in self-imposed exile outside India since 2006, was recently conferred citizenship by Qatar.
"Husain has every right to return to India, but he has to take a decision," the court added.