By making such a statement, the army chief has indulged in politics which is against the constitutional mandate given to him, president of All India United Democratic Front tweeted.
He tweeted: "Gen Rawat has made a political statement, shocking! Why is it a concern for the Army Chief that a political party, based on democratic and secular values, is rising faster than BJP?"
Mr Ajmal's tweets came in response to General Rawat's statement yesterday that AIUDF's growth has been "faster" than that of the BJP in the 1980s. The Army chief was referring to reports of increase in Muslim population in several Assam districts.
Alternative parties like the AIUDF and the AAP have grown because of the misgovernance of big parties, he added.
The MP from Dhubri also tagged the tweets to Twitter handles of Rashtrapati Bhavan and the Prime Minister's Office asking them to "please take note".
The AIUDF, which was formed in 2005 to champion the cause of the Muslim community, currently has three MPs in the Lok Sabha and 13 MLAs in Assam.
Later, Mr Ajmal told journalists that the army chief was "misinformed and misguided".
Mr Ajmal also added he has "full faith" in General Rawat and that protecting the country is his job.
Addressing a seminar in New Delhi yesterday, the army chief had also said that a "planned" influx of people from Bangladesh into the Northeast is taking place as part of proxy warfare by Pakistan with support from China with an aim to keep the area disturbed.
Meanwhile, senior Congress leader and Assam's former chief minister Tarun Gogoi said if the army chief's statement, as reported in the media, is true, what is the centre doing?
"The government should take appropriate steps in this regard as this will be dangerous not only for Assam and Northeast but for the entire country," Mr Gogoi told reporters.
He claimed that the central government has completely failed to secure the country's borders and provide security.