Stafford says that the Al-Sudani newspaper misquoted his remarks, with the newspaper claiming Stafford said that "regime change" would simplify the normalization of U.S.-Somali relations.
"My response to this question was and remains that the Sudanese people decide the form and nature of their government; we accept and respect the choice and sovereignty of the Sudanese people," Stafford said.
Sudan's ruling National Congress Party last Sunday slammed the comments Al-Sundani attributed to Stafford. NCP official spokesman Badr el-Din Ahmed Ibrahim called on the U.S. administration to observe international law and mutual respect for sovereignty in its relations with Sudan.
Stafford, however, reiterated that the U.S. government isn't seeking to remove the current Sudanese government.
"We are at its full disposal to discuss prospects for normalizing relations or any other matter that it wishes to discuss," he said.
Sudanese President Omar al-Bashir is unique among world leaders in that he is the only head of state subject to two arrest warrants issued by the International Criminal Court for genocide committed in the country's rebellious region of Darfur.
The first warrant was issued March 2009 by the ICC for war crimes and crimes against humanity in Darfur. ICC officials issued a second arrest in July 2010 for Bashir, the first time the ICC has issued an arrest warrant for the crime of genocide.
The picture is further complicated by the secession of South Sudan.
Khartoum's revenues dropped dramatically since the departure of South Sudan and Bashir's government is strapped for funds. South Sudan holds three-quarters of the proven oil reserves, which is the main source of revenue for Sudan.
Khartoum, however, has the infrastructure to get the oil to market.
Sudan and South Sudan have wrangled over oil pipeline transit fees in the 14 months since South Sudan became independent.
While until July 2011 the former Sudanese unitary state's daily oil output was approximately 500,000 barrels per day, the majority of which went to China.
U.S. Secretary of State Hillary Clinton visited the South Sudanese capital Juba on Aug. 3 and urged South Sudan and Sudan to end their oil dispute that has brought them to brink of war.
Clinton's visit was the highest-level visit of a U.S. official to South Sudan since its 2011 declaration of independence.
For better or worse, in the wake of Clinton's visit, Sudan says the Obama administration is biased in favor of South Sudan.