Usha Thakur's remarks have drawn barbs from the Congress.
A BJP minister in Madhya Pradesh has alleged that madrasas or Islamic educational institutions are the breeding ground of fundamentalism and terrorism in the country.
Shivraj Singh Chouhan's minister for tourism and culture, Usha Thakur, known for her controversial comments, triggered controversy on Tuesday when she was asked about the status of mid-day meals in madrasas.
State support to madarsas "should come to an end in the country", Usha Thakur told reporters.
Questioned why, she said, "All fundamentalism and terrorists have been bred in madarsas. Entire Jammu and Kashmir was turned into a factory of terrorism".
Her remarks have drawn barbs from the Congress, which said the minister should not accuse without evidence.
Former Minister and Senior Congress leader Sajjan Singh Verma said
Usha Thakur "is a toy in the hands of the RSS".
"A few days ago, she gave a controversial statement against JAYS, then apologized. Now she is saying this about madarsas," he said, referring to the controversy over the minister's remarks on the Jai Adivasi Yuva Shakti last month.
The minister had called the tribal outfit, which formed an alliance with the Congress in the last assembly polls, "anti-national". Then in face of a wave of criticism and calls for her dismissal, she had withdrawn her comments.
"You (Usha Thakur) have your government," Mr Verma said today. "If you have some proof, act against them (madrasas) but do not poison and divide the society in the name of religion, or just try to give a communal color to everything," he added.
The minister, who represents the Mhow seat of Indore district in the state assembly, has been in news in the past also for making controversial statements.
A few years ago, she had demanded that Muslim men be banned from entering the Garba venues during Navratri.
In May last year, she had termed Mahatma Gandhi's assassin Nathuram Godse a nationalist.