Pongte (60), was on his way to Changlang when his vehicle collided with a SUV yesterday, leaving him injured.
He was rushed to the Dhemaji civil hospital, where he was declared dead, official sources said here today.
Pongte is survived by wife, two sons and two daughters.
State Governor Nirbhay Sharma and Chief Minister Nabam Tuki joined the state in mourning the death of Pongte.
The state government declared state mourning today as a mark of respect to the departed leader.
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The national flag flew half mast while a holiday will be declared in Changlang district tomorrow, the day of his funeral, sources said.
"The information has come as shock to me. This is a moment of tragedy and I, on behalf of the state government and the people of the state, convey heartfelt condolences to the bereaved family members," the chief minister said in a message.
Pongte, a footballer, after graduating from JNC, Pasighat, joined the state government as a circle officer in 1978 but resigned in 1984 to plunge into politics.
He had proven his calibre as a student leader since 1968 and served in various capacities including as AAPSU joint secretary (1970) and general secretary (1974-76).