More than 60 people were massacred and 50,000 forced to flee in a series of attacks in Muzaffarnagar last September. India's Election Commission has asked Amit Shah, Mr Modi's aide, to clarify his remarks.
The BJP's opponents seized on the manifesto to exploit fears among Muslims that a Modi government could see a return to the violence that engulfed Gujarat, where he is chief minister, in 2002. More than 700 Muslims were massacred in the riots which led to Mr Modi being treated as an international pariah by Britain, the United States and the European Union.
Since then, as the possibility of Mr Modi being India's next prime minister has increased, London and Washington have lifted the boycott and held a series of meetings with him. His supporters have claimed he has been cleared of any wrongdoing in his handling of the riots, but the ruling Congress Party has accused him of failing to protect Muslims.
Narendra Modi and Rahul Gandhi. Photos / AP
Mr Modi has in turn accused Congress and other opponents of hypocrisy and promised he would bring greater security and prosperity for Muslims, citing the higher living standards they enjoy in Gujarat. He said his government would show "zero tolerance" to terrorists and countries that threatened India's security. "There will be such a strong government at the centre that no country dares to threaten us," he said.
Mr Modi's BJP is aiming to form a coalition with more seats than the ruling Congress-led coalition, which has ruled India since 2004.
The BJP is currently ahead in opinion polls, but the election - with 815 million registered voters - will continue across India's 28 states and seven union territories until May 12.