Suspecting the role of some "hostile forces" behind such incidents, the Minister of State for Minority Affairs said such "tactics" will not be allowed to succeed.
He, however, stressed that the incidents cannot be justified and pitched for tough action against the perpetrators.
Mr Naqvi reiterated the Narendra Modi government's commitment for inclusive growth and creating an atmosphere of trust among the communities.
He said safety of every section of the society was "equally important for" for the Centre.
"I do not think there is fear or insecurity among minorities. But whatever incidents are taking place, be it small or big, be it a criminal conspiracy, in no way it is justified. Action should be taken as per law against them," Mr Naqvi said after attending the 76th meeting of Central Waqf Council in the capital.
On asked which forces were behind such incidents, Mr Naqvi did not name any.
He, however, added that be it political organisations or individuals, the state governments (given law and order is a state subject) concerned were taking "immediate and effective" action against the people involved.
"The governments of Rajasthan, Haryana and Jharkhand have without wasting any time taken action against such people. I myself had spoken to the chief ministers and officials of these states," he said.
Speaking during the meeting, the Union minister said his ministry had been working towards socio-economic-educational empowerment of all the notified minorities -- Muslim, Christian, Buddhist, Sikh, Parsi and Jain -- effectively as a "mission and commitment".
The minister said the measures the Centre had taken during the last three years of its rule were a reflection of its "empowerment without appeasement" policy, which he added, has created an "atmosphere of development and trust".