"There were heavy casualties on the part of the militants," Lieutenant-Colonel Sagir Musa, a military spokesman for the task force in Rivers state, said.
"We are hopeful they will give up the fight very soon."
'Hurricane of retaliation'
He said no oil facilities were affected by two days of heavy fighting.
Violence in the Niger Delta, the centre of the Opec member's oil sector, has halted a fifth of the country's oil production since 2006.
|Insecurity in Niger Delta has cut oil output by around a fifth since 2006 [EPA]
The Niger Delta accounts for most of Nigeria's oil output of two million barrels per day, making it the world's eighth biggest oil exporter.
Dr Muhammed Ali Zainy, a senior analyst for the centre for Global Energy studies, told Al Jazeera: "Recently Opec reduced production by about 520,000 barrels per day but this did not stop the sliding price of oil.
"This means that the demand for oil is faltering and that the world economy is weak, therefore any dent in Nigerian oil production would not have a big impact on the market," he said.
Mend members warned oil firms in the Niger Delta on Saturday to withdraw their workers in the next 24 hours or face a "hurricane" of retaliation following a major gun battle with security forces earlier in the day.
Mend said security forces used helicopters, jet fighters and more than 20 gunboats in Saturday's fighting.
A security source said soldiers from the army, navy and air force were involved in the clashes.
Insecurity in the region has cut the West African country's output by around a fifth since early 2006, when Mend began blowing up oil pipelines and kidnapping foreign workers, helping push up world oil prices.
Royal Dutch Shell, ExxonMobil, Total, Eni, and Chevron, are among the numerous oil companies operating in the Niger Delta.