Worst affected were Angoram, Ambunti and Wosara-Gowi districts.
"Many communities along the river are now completely under water and the levels, which are different depending on the area, aren't receding," Michael Kaprangi, the East Sepik Provincial Disaster Coordinator told IRIN.
With livelihoods based largely on agriculture, families stockpile food and firewood, moving houses inland where possible, or relocate to higher areas when rainwater from the highlands flows downstream, causing the riverbanks to overflow.
Some communities, particularly those on grassland and flood plains, traditionally construct their houses on stilts, often with the option to raise or lower the entire structure depending on each year's level of inundation.
Due to the flooding this year, however, houses have been raised two or even three times higher than normal, and people don't know how to ground the houses to withstand this amount of water, Kaprangi said.
"Those that live here know how to survive, but this year, the level of flooding has really taken us by surprise. We normally get big floods every 10 years, but this one is two years early, and we weren't prepared for it," he said.
"This flooding is very severe," Andrew Rankin, an Oxfam project manager based in East Sepik, agreed. "It started early and the levels are the worst that have happened here in decades. Buildings in some areas were built to handle flooding, but not for a prolonged period like this."
That fact withstanding, local communities remain strong, the aid worker said.
"There are natural inter-community supply chains, with goods being bartered with people from other areas, so this is not a situation where people are without food, but we would like to get rations to those who need additional nutrition, like children and pregnant women."
Communities use canoes to move between villages during flooding, but high water levels and floating debris, including the bodies of drowned livestock, can make travelling on the river dangerous.
Travelling by air is a more timely, if significantly more costly, option, but access to landing areas remains problematic.
"There's just no reliable transport at the moment. We can try to fly in supplies but there is only one airstrip that services these districts, and the pilots can only use half of it, since the rest has been blocked off by a landslide," Kaprangi said.
With water levels not expected to subside until June, concern remains over possible health risks.
According to the World Health Organization (WHO), malaria is a leading cause of illness and death in PNG. More than 1.6 million cases of the vector-borne disease were reported in 2008, with over 600 deaths.
The disease is endemic to East Sepik, and though organizations such as Rotarians Against Malaria have distributed mosquito nets to communities along the river over the past year, Rankin warned that access to malaria treatment in flood-affected communities remained a challenge.
"An increase in cases of malaria is a huge risk out here," Rankin said, citing concerns over the spread of other diseases as well.
"The number of cases of diarrhoea has risen. We have also just gotten over a cholera outbreak [http://www.irinnews.org/Report.aspx?ReportId=88817] in these areas, but now with the floods, there are new cases. Our main focus right now is finding ways to get treatments out to these communities," he said.
Provincial authorities agreed, and were also preparing medication and mosquito nets for distribution once the floods receded.
"Flooding in PNG may now last longer or cover more areas. We need to start talking about climate change, and how to cope with more severe and frequent flooding," Kaprangi said.
"What we're really concerned about right now though," Kaprangi said, "is what happens when the water goes down."
According to the UN Office for the Coordination of Humanitarian Affairs (OCHA), as flood waters recede in the upper Sepik, water levels in the lower Sepik - including Angoram District - will likely not subside until some time in June.