In an interview to PTI, the former BJP president said the government was focused on 'Sabka Saath, Sabka Vikas' (Together with all, Development for all) and its policies have not discriminated against religious minorities.
"Any saffron clad person on television is immediately related to us (BJP) whereas the fact is that we don't have any relation with that person," he said. "We don't support such people."
Gadkari said violence in the name of protecting cows "should not have happened".
Stating that it was not fair to link such groups with the BJP, he alleged that the move was part of a Left campaign to malign the party and project it as anti-minority and anti- Dalit.
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Certain sections of 'Gau rakshaks' (cow protectors) have reportedly stopped vehicles, beaten people, extorted money and in some cases stolen animals -- all in the name of protecting cows. This has inflamed tensions, risking undermining Prime Minister Narendra Modi's efforts to focus on economic advancement.
"BJP, VHP, Sangh (parivar) and our government do not support such elements," Gadkari said, adding that the party was, however, against cow slaughter.
It a matter of belief, he said, adding that he himself uses 'gomutra ark' or cow urine for therapeutic purposes.
He said such incidents of violence had happened in the past as well during Samajwadi Party and Congress rules.
"Our government has not discriminated against any caste, creed or religion in the last three years," he said.
"Our fight is against poverty, hunger and disease. Poor is poor and cannot be discriminated against on caste, creed, religion and language.
"We have not lent our shoulders to anyone for use against minorities," he said.
Indians, he said, are genetically tolerant as was reflected in 4,000 year history when not a single mosque was demolished. "We do not discriminate.