Selective intolerance was not good for democracy, he told the party's national executive here.
Shah's remarks come against the backdrop of political violence in Kerala and West Bengal and the killing of journalists in Bengaluru and Tripura.
Certain acts of intolerance were glossed over and some others were passionately debated, a party statement quoted Shah as saying.
"When our workers are killed in Kerala or West Bengal, when atrocities take place against them, when Kashmiri Pandits are evicted, then intolerance is not talked about. But whenever we approach elections, intolerance is hotly debated.