Authorities in Twic and Tonj states said civil servants have started receiving their salary arrears not paid since May this year.
Speaking to Radio Tamazuj on Friday, Twic State Information minister, Michael Mayot said the pay will cover five months.
He pointed out those months to be covered are May, June, July, August and September.
Separately, Tonj State Information minister, William Wuol Mayom also confirmed the salary payment, adding that the money came from the finance ministry in the capital, Juba.
In a speech to mark Independence Day in July, President Salva Kiir apologised to the civil servants who went without salaries for several months, saying the failure was "caused by weak governance" in the departments supposed to raise the funds and pledged to personally get involved.
South Sudan heavily relies on oil revenue to fund its budget.
The Petroleum ministry said it plans to increase output to more than 350,000 barrels of crude per day by the middle of 2020, up from the current 180,000 barrels per day, according to official figures.