The arrests saw the government being dubbed "undemocratic", which was underlined over the weekend after a farmer was arrested for criticising the chief minister.
The rights body found two police officers, who booked Mahapatra, guilty of harassment and recommended departmental proceedings against them.
The government has been given six weeks to comply with the order. But there is a chance that it might be ignored, since the rights body only has advisory powers.
"I believe the officers acted under pressure. Unless the real culprits are arrested, I won't get justice," said Mahapatra.
The government should withdraw the case against him, he said.
The row:Cartoon a conspiracy, prof an offender: MamataCartoon arrests: Nation responds with outrage