In both regions “you have people who for a long time have felt that they want their secular governance and identity respected”, Kerry told reporters on the sidelines of an African Union summit.
The US top diplomat insisted people in the war-torn areas – where rebels are battling government troops – did not want independence or to “break away from Sudan”.
“Unfortunately President Bashir is trying to press on them through authoritarian means and through violence an adherence to a standard that they simply don’t want to accept with respect to Islamic” law, Kerry added.
Khartoum was also showing “a rigidity with respect to their identity”, he said.
“So that’s the fundamental clash, and what is critical here in my judgement is for President Bashir to respect what the people in South Kordofan and Blue Nile are trying to achieve,” Kerry said.
New US envoy
But speaking ahead of talks in Addis Ababa with the Sudanese Foreign Minister Ali Ahmad Karti, Kerry also acknowledged that South Sudan’s alleged support for the SPLM-North rebels fighting in the two regions worried Sudan.
South Sudan separated from Sudan in 2011 after decades of bloody civil war, but still unsettled issues over border areas and oil have continued to flare into clashes.
Kerry announced after talks with Ethiopian Prime Minister Hailemariam Desalegn that he would soon appoint a new US envoy to Sudan and South Sudan to replace Princeton Lyman.
“I think North and South are in a very delicate place right now…. It is important to build on the peace process, and build on the independence of the young state and put the focus and energy on the people and developing the future and not fighting the issues of the past,” he said.
South Kordofan is part of Sudan but its people fought alongside the now independent South Sudanese army during the 1983-2005 civil war.
More than 200 000 people have fled the war zone for South Sudan and Ethiopia as refugees, while an estimated one million more have been affected inside South Kordofan and Blue Nile, where renewed fighting broke out nearly two years ago.
Special challenge
Kerry also called for all residents of the flashpoint zone of Abyei, which straddles the border between Sudan and South Sudan, to be allowed to vote in a long-delayed referendum.
Abyei’s status is the most sensitive issue left unsettled by the peace treaty between the two states.
The territory was to hold a referendum in January 2011 on whether it belonged with Sudan or South Sudan, but disagreement on who could vote stalled the ballot.
“Abyei presents a special challenge and I think we agree that it is critical that Abyei be able to have a referendum,” Kerry said.