The decision to expel Mary Cummins was made in a state Cabinet meeting, deputy state governor Mabek Lang told The Associated Press.
Cummins is head of the UN mission in Unity state. UNMISS' human rights division released a report on June 30 accusing government forces of committing human rights abuses, including killing women and children, gang rape and burning people.
UNMISS acting spokesman Joe Contreras said that the mission is aware of reports that the mission's top official in Unity state shouldn't return to her duty station.
In May, South Sudan expelled UN humanitarian coordinator Toby Lanzer. UN Secretary-General Ban Ki-moon, through a spokesman, condemned the government of South Sudan for its decision to expel Lanzer, saying he has been instrumental in addressing the increasing humanitarian needs in the country.
South Sudan, which on Thursday marked four years of independence, has been plagued by violence since December 2013 as government troops battle rebels led by a former deputy president.