Brigadier-General Elias Zamani, commander of a task force set up to protect oil facilities in the Niger Delta, said that his men protecting the Benisede flow station south of the port city Warri had come under fire at dawn.
Military officials refused to give details of casualties, but Shell said that five of its staff had been injured and evacuated to Warri, while a witness told Agence France Presse that he had seen at least three troops shot and injured.
"Heavily armed persons ... attacked the SPDC Benisede flow station in Bayelsa State," said a statement issued by Shell on behalf of its Nigerian subsidiary, the Shell Petroleum Development Company (SPDC).
"The attackers invaded the flow station in speed boats, burnt down two staff accommodation blocks, damaged the processing facilities and left.
"Following the growing insecurity in the area, SPDC has commenced evacuation of personnel on duty from Benisede, and neighbouring flow stations," it added.
Four kidnapped
The attack came five days after a group of gunmen kidnapped four oil workers and blew up the pipeline connecting Benisede and the nearby Opukushi, Ogbotobo and Tunu flow stations to the Forcados export terminal.
The hostages, an American, a Briton, a Bulgarian and a Honduran, are thought to have been hidden in the swamps close to the site of Sunday's attack.
Both the kidnapping and the pipeline blast have been claimed by a previously unknown separatist group dubbed the Movement for the Emancipation of the Niger Delta, which seeks independence for the region's 14-million-strong Ijaw people.
The group has demanded the release of two local champions, including Ijaw guerrilla leader Mujahid Dokubo Asari, and warned in an e-mail statement: "We are capable and determined to destroy the ability of Nigeria to export oil."
Benisede is a riverside pumping station, which gathers crude oil from a network of wells in swampland around the Bomadi Creek, part of the Niger Delta 300 kilometres southeast of Lagos.
The plant is routinely guarded by a platoon of Nigerian soldiers from Zamani's Joint Task Force, a combined unit set up to protect the Niger Delta's multi-billion-dollar oil industry from attack by pirates and militias.
Navy spokesman Captain Obiara Medani said that security forces were still trying to locate the kidnappers in the creeks south of Warri, but that any negotiations were a "political matter" that he could not discuss.
"We are making progress as to their location," he said.
Crippling poverty
Although Nigeria is Africa's biggest oil producer, pumping around 2.6 million barrels per day worth billions of dollars, most Nigerians still live in crippling poverty, especially in the remote creeks of the delta.
This Scotland-sized swathe of mangrove forest and heavily wooded swampland, is home to several heavily armed pirate gangs and militant groups. Kidnappings and sabotage are common.
Asari declared a ceasefire in August 2004, but vowed to win Ijaw independence and control over the delta's oil through political agitation.
He was arrested last year after threatening to tear Nigeria apart and will appear in court on Tuesday charged with treason. Asari's lawyer, Uche Okwukwu, insists his group has no link with the recent attacks.