More than 8,000 rebel fighters laid down their arms and accepted the amnesty which ran from August 6 to October 4.
The offer was to help check years of unrest which is preventing Nigeria from realising two-thirds of its oil capacity, and the unconditional pardon of Mend members is the most serious attempt yet by the government.
But Mend, with an estimated 10,000-strong force, dismissed the amnesty as a "charade", saying it failed to address key issues of under-development and injustice in the Niger Delta.
Last week the group warned it would "burn down" all previously attacked oil installations.
"In this next phase, we will burn down all attacked installations and no longer limit our attacks to the destruction of pipelines," it said in an email.
But the group has been weakened after its senior commanders and thousands of others accepted the amnesty and disarmed.
Claiming to fight for a fairer distribution of the region's wealth, Mend fighters have repeatedly attacked oil infrastructure and government forces across the delta in the past three years, forcing down output from 2.6 million barrels a day to 1.7 million and putting Nigeria's position as Africa's top oil exporter at risk.
The central bank says the disruptions cost Africa's most populous nation $1bn a month in lost revenue.
Despite Nigeria's oil riches, the vast majority of its 140 million people live on $2 a day or less, and some of the most acute poverty is in the villages of the delta.