"We confirm that the airport in Mbandaka has been attacked by insurgents who arrived by boat," Mounoubai said.
"We think [the fighters] are the Enyele, a group that started fighting six months ago claiming fishing rights, but now they are far from their land and we don't know what they want," Mounoubai said.
The Enyele are embroiled in a dispute with the Monzaya over fishing rights in nearby lakes.
The fighters, that UN sources said numbered at least 30, were forced out of the town and towards the airport by more than 100 DR Congo soldiers.
"There are many of them and they took us by surprise but we chased them and they fled to the airport," General Janvier Mayanga, operational commander of the Congolese army, told the Reuters news agency by telephone from Mbandaka.
"We've already started the counter-attack to take back the airport," he said.
UN peacekeepers and contractors at the airport and at a fire station beside it - both about 7km from the riverside governor's residence - retreated into the surrounding bush.
UN and army sources could not confirm whether there were any civilians killed in the fighting, but sources in the area said hundreds were sheltering in churches after Easter Sunday services.
A resident of Mbandaka contacted by telephone by the AFP news agency said there was still sporadic gunfire in several neighbourhoods and claimed that soldiers had looted property in the town.
More than 200,000 Congolese have fled their homes in Equateur in the past six months due to the violence between the Lobala and Boba tribesmen, Refugees International, an aid agency, said.
Officials said the latest assault in Mbandaka was thought to be separate from an ongoing conflict between UN-backed forces and rebels in Congo's east.
Monuc is the largest peace keeping operation in the world with 22,000 soldiers, but it has been criticised for failing to prevent frequent attacks on civilians.