Modi, the prime ministerial candidate of the Bharatiya Janata Party (BJP), is running on a platform to revive an economy going through the worst slowdown since 1980s.
But half-way through a five-week campaign to win over the country's 815 million voters, some members of the BJP and its hardline affiliates are facing accusations of trying to whip up a partisan agenda.
"Petty statements by those claiming to be BJP's well wishers are deviating the campaign from the issues of development & good governance," Modi, the biggest campaigner for the party, said in a Twitter post.
"I disapprove any such irresponsible statement & appeal to those making them to kindly refrain from doing so."
On Saturday, Giriraj Singh, a leader of the Bihar state wing of the party, said those opposed to Modi would have to leave India and go to Pakistan after the BJP won the election and formed a government.
A couple of days later, television channels showed a video in which Praveen Togadia, a firebrand member of the Vishwa Hindu Parishad, a sister organisation of the BJP, was seen offering advice on how to prevent Muslims from buying property in Hindus-dominated areas.
Togadia denied that, saying he only asked Hindus to seek the help of police to resolve property disputes involving Muslims.
The statements, however, have re-ignited concern about religious minorities under a BJP government, which rivals say has a deep-seated bias against India's 150 million Muslims.
Modi himself is tainted by accusations that he encouraged or turned a blind eye to Hindu-Muslim riots in 2002 in Gujarat, the state he has governed for 13 years. More than 1,000 people, most of them Muslims, were killed in the violence.
He has always denied the accusations and a Supreme Court inquiry did not find evidence to prosecute him.
"These crocodile tears ... will not do," said Abhishek Manu Singhvi, a leader of the ruling Congress party, referring to Modi's Twitter posts criticising colleagues' statements.
"People know the truth."
While opinion polls are predicting Modi's BJP-led alliance will win the biggest chunk of the 543 parliamentary seats being contested in the election, that ends on May 12, most of them show he will need allies after the polls for a majority.
An anti-Muslim pitch is not only expected to make it tougher for him to find coalition partners, but could also drive away some of middle-class voters, whose support Modi is banking on to unseat the Congress party.
But some of Modi's colleagues remain defiant.
BJP leader Singh, who is contesting the election in Bihar, said he stood by his statement. "I have said what I felt. I will give my explanation."
This month, the election commission banned one of Modi's top aides from election rallies on charges of making inflammatory speeches against Muslims.
The ban was lifted last week after the aide, Amit Shah, vowed not to use abusive or derogatory language. The commission said that it would monitor his campaigning.
Separately, a leader of the BJP's alliance partner in the Western state of Maharashtra said on Monday Modi would teach a lesson to Muslim rioters. Shiv Sena leader Ramdas Kadam made the comments at a joint election rally with Modi in Mumbai.