The outbreak has mainly affected displaced residents in the Kitgum district returning to their homes, which lack proper hygiene, said Kenya Mugisha, the ministry's director for clinical services.
"These people are moving from IDP camps to areas with no facilities. They have poor hygiene and sanitation," Mugisha told AFP, adding that 836 new infections have been reported since August 14.
Northern Uganda is 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 residents have started returning to their native villages.
Hepatitis E has a low mortality rate compared with hepatitis B and C and is spread by eating contaminated food or drinking water.