Martin Elia Lomuro, South Sudan's minister of cabinet affairs, said the decision was taken "to address the challenges that impede the implementation of the peace agreement".
Nearly nine million people will need aid this year in South Sudan, according to the UN, as the world's youngest country struggles with a food crisis and rising violence.
The executions were allegedly in response to a 22 July attack by the South Sudan People's Movement/Army on the Mayom county commissioner, the United Nations said.
South Sudan's National Security Services have made credible threats on some people's lives, causing them to flee the country, according to a UN commission.
The Khartoum Declaration, for a ceasefire in South Sudan, will take effect within the next 72 hours, raising hopes for an end to one of Africa's most devastating civil wars.