"The way the Mayawati government slapped National Security Act and jailed Varun is a bid to appease Muslim vote bank. It is a warning to Hindus," Thackeray was quoted in an editorial in Sena mouthpiece Saamana.
"We can understand that action was taken for his alleged remarks but what is the justification for invoking NSA and putting him behind bars for a year," Thackeray said.
How could Indira Gandhi's grandson pose a danger to the country, the Sena chief asked.
"If what he said poses danger to the country then arrest 80 crore Hindus under NSA," he added.
"Nobody ever thought it was a danger to the country's security when Sonia Gandhi continued to live in Indira Gandhi's household for 17 years without accepting Indian citizenship," he said.
"Lakhs of Bangladeshis illegally enter India. Congressmen make them voters and win polls. Nobody thinks that the rapidly multiplying population of Muslims who abhor family planning is a threat to national security. But a youth who is yet to grow a moustache is termed a threat to the country," Thackeray said.
The National Security Act was invoked against Varun Gandhi, who had been booked for making anti-Muslim speeches, last Sunday.