The U.S. State Department warned that clashes between forces loyal to the government in Khartoum and those supporting the south's Sudan People's Liberation Army have resulted in heightened security concerns.
Fighting in May and June along the north-south border prompted the U.N. Mission in Sudan to evacuate non-essential staff from the region. Frequent clashes continue in Southern Kordofan state, which is situated along the regional border.
Thousands have fled the border region of Abyei after northern forces occupied the region.
In Darfur, Westerners are at risk of kidnapping and other violent crimes, the State Department warning adds. That holds for Juba, the southern capital, as well.
"If you are affiliated with humanitarian relief or development efforts in southern Sudan or Darfur, you should take prudent measures to reduce your exposure to violent crime and should adhere closely at all times to the security policies and procedures of your organization," the warning read.
South Sudan becomes an independent state July 9 following a January referendum that was part of a peace agreement reached in 2005.
The international community has expressed concern that recent conflicts threaten to undermine substantial efforts at establishing peace in the region.