The Sahara chief was arrested on Friday after he failed to appear before the judges in connection with a fraud case.
Two Sahara firms were ordered to repay 240bn rupees ($3.9bn; Â£2.3bn) to investors that market regulators said they had raised illegally.
On Tuesday, a protester threw ink on Mr Roy's face as he arrived at the court.
"Subrata Roy is a thief. He has cheated and robbed us," his attacker shouted. The man, identified as a lawyer by Indian television channels, was taken away by the police.
Profile: Subrata Roy
It was not immediately clear whether the businessman would now be sent to jail. Since his arrest, he has been lodged in government guest houses.
The Supreme Court set the next hearing for 11 March.
On Tuesday, Mr Roy apologised to the court saying his reasons for not appearing before the judges last Wednesday "were genuine".
He said Sahara would sell its assets and pay back the investors and asked the judges to give him more time.
But the court rejected his proposal saying "we are not interested in selling the properties, you have been telling us for the last two years, it is your headache, you should have done it".
The judges also ordered police to take two other Sahara directors into custody and hold them until the next hearing.
The case against Mr Roy stretches back to August 2012, when the court ordered the two Sahara firms implicated to refund money to 22 million small investors within 90 days and with 15% interest.
In December 2012, the court gave the firms more time to repay.
In February last year, market regulators  froze the firms' bank accounts saying they had failed to refund the money.
But Sahara disputes the amount it should pay back, saying its liability should be no more than the 51.2bn rupees it has already paid back.
Mr Roy is a household name in India.
His group, worth $11bn, has businesses ranging from finance, housing and manufacturing to aviation and the media.
It also has interests overseas - it owns New York's landmark Plaza Hotel and London's iconic Grosvenor House.
Sahara also sponsors the Indian hockey team and owns a stake in Formula One racing team, Force India.
With more than 1.1 million workers, the group is India's biggest private sector employer.
India's Supreme Court has ordered the continuing detention of businessman Subrata Roy and asked his firm to come up with a plan to repay its investors.