Union Home Minister Rajnath Singh and BJP president Amit Shah were present during the oath-taking ceremony of the National People's Party (NPP)-led government.
In last assembly elections, 90.57 per cent polling was recorded in Nagaland and 89 per cent in Meghalaya.
Buoyed by the formation of governments in Assam, Manipur and Arunachal Pradesh, the BJP is making a determined bid to expand its footprint in the north-east.
Speaking at a rally in poll-bound Meghalaya, Rahul Gandhi said the BJP-led government had failed to create jobs for youth and fair prices to farmers for their produce.
Rajnath Singh said the incident indicated "utter chaos and lawlessness" in the northeastern state while Nationalist Congress Party (NCP) leader Vijaj Raj said it was a "political murder".
Sangma had only recently joined the NCP having come close to winning the Williamnagar seat in the previous Assembly Elections in the state in 2013.
"They (BJP) came to power in 2014 with promises to the people but they could not keep any of these promises and people are upset with them," he said.
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