Human Rights Watch (HRW) warned on Thursday that Khartoum was "taking a terrible step backward" despite having signed a peace accord with rebels to end 21 years of civil war in the south.
"The government's campaign of ethnic cleansing in Darfur raises real questions about whether Khartoum is really willing to comply with Wednesday's peace accord in the south," their statement said.
The rights watchdog added that pro-government militias had attacked five villages 15km south of Nyala in Darfur as recently as last Tuesday.
The raids killed 46 civilians and wounded at least nine others, the statement said, citing local sources.
The group has documented how the Janjawid have been armed, trained, and uniformed by the Sudanese government.
Agreement in south
Meanwhile, Khartoum and the southern-based rebel Sudan People's Liberation Army (SPLA) signed agreements on the last outstanding issues barring the way to a definitive end to the civil war on Wednesday.
The agreement came after marathon talks between Vice President Ali Usman Taha and SPLA leader John Garang that started in September 2002.
"The government's campaign of ethnic cleansing in Darfur raises real questions about whether Khartoum is really willing to comply with Wednesday's peace accord in the south"
Human Rights Watch statement
But HRW said: "Darfur remains a cloud over Sudan and it would be inappropriate for the United States to hold a high-level celebration of the peace accord while the ethnic cleansing continues in western Sudan."
Late Wednesday, US Secretary of State Colin Powell also tempered his praise for the peace accord by saying: "Sudan will not be at peace until the problem of Darfur is resolved."
Khartoum has faced mounting international anger over the humanitarian crisis in the western region.
The government has been accused of operating a scorched earth policy in the face of the rebellion launched by members of the Fur, Massalit and Zaghawa minorities in February 2003.
At least 10,000 people have been killed and more than a million driven from their homes.