In its first public criticism of President Muhammadu Buhari, the Movement for the Emancipation of the Niger Delta (MEND) said he was "jeopardizing the fragile peace in the region" with public comments about the unrest while reneging on past agreements.
MEND had backed Buhari in his 2015 presidential election campaign and urged militants behind the most recent spate of attacks to pursue peace talks with the government.
The attacks in the OPEC member's energy hub, coupled with low oil prices, have helped to push Africa's biggest economy into recession - the first in 25 years. Crude oil sales account for two-thirds of government revenue.
Those behind the attacks, which began in early 2016, say they want a greater share of Nigeria's energy wealth to go to the southern region. The frequency of attacks has reduced since Buhari held talks with community leaders but there are sporadic attacks, most recently in late November.
MEND, which was one of largest militant groups until it signed up for a government amnesty in 2009, said in a statement emailed on Sunday that it had passed "a vote of no confidence" in Buhari's government.
It said he should tell government agencies to "immediately commence dialogue with the Niger Delta region" but did not say what it would do if the approach to the peace process was not altered.
MEND's members are influential in the Niger Delta but it is unclear whether this extends to those responsible for the most recent attacks because the militant scene is splintered into small groups which each have their own list of demands.
The presidency declined to comment on MEND's statement. Buhari said in his New Year's message on Saturday that he will seek a peace settlement in the oil-producing region.
The attacks cut Nigeria's oil production, which stood at 2.1 million barrels per day (bpd) at the start of 2016, by more than a third in the summer although the oil minister said repairs to oil facilities lifted output to nearly 1.8 million bpd in December.