0844 GMT April 03, 2020
President Salva Kiir had said he would compromise by cutting the current 32 regional states back down to the original 10 – a key rebel demand – to pave the way for a unity government, AFP reported.
But Kiir also included on top of the 10, three "administrative areas" of Pibor, Ruweng and Abyei.
Rebel chief Riek Machar said he opposed those three areas, saying it "cannot be referred to as reverting to 10 states" and "as such cannot be accepted".
"We therefore call upon President Kiir to reconsider this idea of creating administrative areas," he said in a statement.
Machar warned the three areas risked causing further problems, calling the issue a "Pandora's box."
Kiir and Machar – who lives in exile – are under increasing international pressure to resolve their differences before a February 22 deadline.
Machar has repeatedly said he could not return to his old job as vice-president if country's structure of states did not return to its original form.
The number of states is contentious because the borders will determine the divisions of power in the country.
When it gained independence from Sudan in 2011, South Sudan had 10 states, as set out in its Constitution.
Kiir increased that in 2015 to 28, then 32 – and has now reduced them back to 10, plus the three areas.
He issued an order late Saturday relieving all governors of the 32 states of their posts.
He has said the final matter of states would be debated once the unity government forms.
Of the three areas, the most contentious is thought to be oil-rich Ruweng, in the north.
Oil provides almost all of the government's revenue in South Sudan, one of the world's most oil dependent nations.
Ruweng has been one of the most heavily fought over areas in the civil war and is claimed by both the Dinka people of Kiir and the Nuer of Machar.
Abyei, another of the three areas, is a border zone contested with neighboring Sudan.
Pibor lies in the eastern Jonglei region, an area long troubled by militias and rebels fighting over local grievances.
Kiir and Machar are old rivals who have fought and made up multiple times.