Asma Jahangir, the UN special rapporteur on executions, said on Sunday that her accusations were based on "credible information".
She also said members of the militia, which locals accuse of looting and killing villagers, were being integrated into the armed forces.
Jahangir made the comments after visiting the conflict-stricken Darfur region.
Independent rights groups have already accused the government and militia, known as janjaweed, of carrying out mass executions in the region where rebels launched an armed uprising in February 2003.
Fighting in the remote area has affected two million people and driven 158,000 people across the border into Chad, creating what the UN has said is one of the world's worst humanitarian crises.
"I received numerous accounts of the extrajudicial and summary executions carried out by government-backed militias and by the security forces themselves," Jahangir told reporters.
"According to credible information, members of the armed forces, the Popular Defence Forces and various groups of government-sponsored militias attacked villagers and summarily executed civilians," she said in Khartoum.
"I received numerous accounts of the extrajudicial and summary executions carried out by government-backed militias and by the security forces themselves"
UN special rapporteur on executions
Rights groups have accused the government of arming the Arab janjaweed to drive out African villagers from their homes, in what UN officials have said is a campaign of ethnic cleansing.
The government calls the janjaweed outlaws and denies any link.
"According to the information I collected, many of the militias are being integrated into the regular armed or the Popular Defence Forces. There is no ambiguity that there is a link between some of the militias and government forces," Jahangir said.
But she said some criminal elements had taken advantage of the conflict.
Jahangir also travelled around other areas of Sudan, including Malakal in the south. The Sudanese government is close to reaching a final peace deal with southern rebels to end a separate 21-year-old conflict in that region.
"In my report, I will forcefully stress the question of accountability as a fundamental principle in addressing violations of human rights... The government of the Sudan must make every effort to end the culture of impunity," she said.