The Kerala state legislative assembly adopted a motion on Monday demanding protection for people's livelihoods and the removal of the lawmaker, Praful Patel.
Adding to the bad feeling, a protest against a local official's comments on drug abuse resulted in 23 arrests, according to Indian media.
It was the first phase of voting in both states, and the results won’t be known for months.
Modi and his home minister Amit Shah campaigned aggressively for their Bharatiya Janata Party in West Bengal, luring local politicians away from the Trinamool Congress (TMC) party, whose firebrand leader Mamata Banerjee has been chief minister since 2011.
“We need more doctors, police officers, bureaucrats, and teachers, from the minority Muslim community rather than imams for mosques,” Assam’s education minister said.
More than 700 of the madrasas in Assam will be closed by April.