NDPVF's Mujahid Dokubo-Asari was jailed for treason and freed in 2007
Hours after an amnesty for Nigeria's oil militants expired, the original group that began the unrest has gone to court, arguing the move is illegal.
The 60-day amnesty offered cash and training for fighters who disarmed.
A lawyer for the Niger Delta People's Volunteer Force told the BBC he feared government forces would now "unleash terror" in the poverty-stricken Delta.
A BBC reporter says the group has been inactive for a few years, but its case may be intended as a rallying call.
Most prominent militant leaders have accepted the amnesty - part of government efforts to end years of attacks on the Nigerian oil industry.
But the BBC's Ahmed Idris in the capital, Abuja, says some militants in the oil-rich creeks are unwilling to give up their arms and lucrative oil-stealing business.
There is nothing to forgive here if you are fighting for the self-determination of your people
NDPVF lawyer Festus Keyamo
Will amnesty bring peace?
Profile: Mujahid Dokubo-Asari
The reverend Stephen Davis, a former adviser to two Nigerian presidents on the Niger Delta, also has doubts about the amnesty, saying that the underlying political and economic landscape has not changed.
He says there are still no jobs for disaffected youths, powerful people in Nigeria continue to make money form oil theft and political godfathers will still need young men with guns in order to secure their positions.
The officials behind the amnesty have branded Reverend Davis "a mischievous nay-sayer".
But a government spokeswoman argued that jobs and economic development would come now there is peace and security.
NDPVF lawyer Festus Keyamo told the BBC the amnesty deal was a calculated plot to divert attention from the region's under-development and right to self determination.
"They [NDPVF] are saying: 'Give us our resources to control, you have no right to control our resources on our behalf and no amount of intimidation or amnesty can make us lose focus of that fact,'" he said.
In the papers filed at the Abuja High Court, the group says President Umaru Yar'Adua does not have the power to grant pardons when nothing has been done wrong.
"Amnesty means 'We forgive you', but there is nothing to forgive here if you are fighting for the self-determination of your people," Mr Keyamo said.
He also said the group saw the amnesty "as a means to cow everybody in the Niger Delta into submission and silence".
NDPVF leader Mujahid Dokubo-Asari was an ethnic Ijaw leader who began fighting the government in 2003.
He took up arms after accusing Niger Delta politicians of failing to pay him and his group for helping to rig elections in that year.
He was jailed for treason in 2005 and during his two years in prison most of his fighters joined other groups in the oil-rich swamps.
Since his release he has lived in the capital.
Although Nigeria is the world's eighth-largest oil exporter, the unrest has prevented it from pumping much more than two-thirds of its production capacity.