The virus, concentrated in the Kitgum district which is home to numerous camps for civil-war displaced, has caused 6,762 infections, with 232 new cases reported last week alone.
"The biggest problem has been personal hygiene, which is far below standards," said Joseph Wamara, an epidemiologist with the health ministry. "Many of these people have been confined to camps for years."
Northern Uganda is barely emerging from two decades of civil war and its tens of thousands of displaced inhabitants still living in camps are particularly vulnerable.
Since a fragile truce brought an end to the violence two years ago, some have started returning to their native villages but the condition of their homes there is also part of the problem, Wamara explained.
"None of the amenities are in place," he said referring to the lack of adequate latrines and the limited availability of clean water.
Hepatitis E most often spreads by eating food or drinking water contaminated with feces of an infected person. There is no vaccine for the disease.
According to a World Health Organization (WHO) report, approximately 70 percent of the deaths have occurred among pregnant women.