Congress is contesting in 19 seats in the February 27 election for the 60-member Assembly. Twenty of its candidates had filed nomination but one of them withdrew candidature.
"The decision is aimed at stopping the BJP and its alliance partner from compromising the rights of our people and our way of life," the Nagaland Pradesh Congress Committee (NPCC) said in a statement.
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The Congress has directed its rank and file to back secular party candidates to save the people from sinking in the "Hindutva quicksand," the Congress statement said.
The BJP has formed an alliance with the Nationalist Democratic Progressive Party (NDPP) led by three times former chief minister and sitting MP, Neiphiu Rio. The BJP and the NDPP would contest in 20 and 40 seats respectively.
The Congress welcomed secular minded parties and leaders to form a broad consensus to provide a secular and stable government and to stop the Hindutva forces in the state.
The party also expressed shocked at formation of the alliance between the BJP and the NDPP.
"It is also shocking that the NDPP decided to share Nagaland Assembly seats with the BJP by providing them 20 seats ignoring the cry and fear of the people," it said adding that the NPCC has been campaigning about "the danger of Hindutva for over two and a half years".
The NDPP leaders are all fully aware of how minorities and minority religions are persecuted and are suffering under the BJP rule, the statement said.