Sources from the ethnic Ijaw group said on Friday that rival Itsekiris had sparked the new violence with a waterborne attack.
"Between two and four (in the afternoon) Itsekiri youths went in a convoy of 36 speedboats to launch an attack on the Ijaw community of Ojudorgbene," local human rights activist Joel Bisina told Reuters.
"Following that attack a military helicopter went to another community known as Ububarakiu and opened fire ... and killed four people."
A local official from the Itsekiri ethnic group said there had been "some fighting and some killings" but could not provide further information. Military officials were not available for comment.
Daniel Ekpebide, a member of the armed group Federated Niger Delta Ijaw Communities, put the death toll from the ethnic clashes and the army raid much higher, at a minimum of 50.
"We are not going to fold our arms and watch the Itsekiri people kill us," he said, adding that the Itsekiris had threatened further attacks in the area.
The southern Niger delta has seen an upsurge of violence since March, when Ijaws launched a rebellion against Itsekiris, the army and oil multinationals.
At its height the rebellion cut off around 40% of oil production capacity in Nigeria, the world's seventh largest exporter and a major supplier to the United States. 10% of capacity remains shut off by the unrest.