Mend said in a statement on Monday that the "depot and loading tankers moored at the facility" were set alight after its fighters carried out the "unprecedented attack".
"We encountered some slight resistance from the Nigerian navy guarding the facility but they were easily overpowered. Over nine may have been injured or killed," it said.
Government, military and oil industry officials confirmed that the Atlas Cove Jetty had come under attack.
Ken Odaga, a villager who lives near the facility, said he heard a "huge boom" at about 10:45pm on Sunday.
"I saw three speed boats with militants off the coast. They were fighting with the naval officers with guns. Next there was an explosion with big smoke," he told The Associated Press news agency.
"I've never experienced that before ... It was like a war between the militants and the naval officers."
It took rescue workers around six hours to extinguish the fires that were apparently started after explosives were used to destroy part of the facility.
Until now, Mend has largely concentrated its campaign on oil facilities and government targets inside the delta region.
Umaru Yar'Adua, the president, agreed to drop treason and gun-smuggling charges against Okah after he accepted the government's offer of an amnesty.
|Okah had been facing charges of treason
and gun-smuggling [File: AFP]
"Having reviewed what the attorney general said, you have become a free man at this moment. You are now discharged," judge Mohammed Liman told Okah at a hearing in the central city of Jos.
Some groups had said they would lay down their arms after Okah's release, but Mend was not among them.
Abubakar Momoh of Lagos State University questioned whether the amnesty could achieve any significant success in halting the violence.
"What the government has done in the case of Okah is like treating the symptom and not curing the disease," he said .
"That will not put an end to militancy there because there are many Henry Okahs there.
"There are issues that drove the militants to the trenches. Until those issues are resolved in a fair and just manner, there will never be peace in the Niger Delta."
State-run Nigerian National Petroleum Corporation (NNPC) says that monthly oil revenue this year has dropped to around $1bn from an average of $2.2bn in 2008.
Nigeria relies on oil for more than 90 per cent of its export earnings.