"It makes me very angry to be sitting there with their president and have this happen," she said. "They have no right to push and shove."
Rice made her remarks to reporters after she and her entourage were on board a plane preparing to leave the Sudanese capital.
"Diplomacy 101 says you don't rough your guests up," Rice senior adviser Jim Wilkinson had said earlier as he and reporters travelling with Rice faced off with guards at the ultra-high-security residence of Sudanese President Omar al-Bashir.
Al-Bashir's guards elbowed Americans and tried to rip a tape away from a US reporter.
At another point, Rice's interpreter and some other aides accompanying her were blocked at a gate.
Rice accused al-Bashir's guards
of manhandling her aides
Ambassador Khidair Haroun Ahmed, head of the Sudanese mission in Washington, attempted to smooth over the situation.
"Please accept our apologies," he told reporters and Rice aides. "This is not our policy."
But there was yet another scuffle with security shortly after he apologised when a US television reporter tried to ask al-Bashir a question about his involvement with alleged atrocities.
Guards grabbed the reporter and muscled her towards the rear of the room as State Department officials shouted at the guards to leave her alone.
The session at al-Bashir's residence capped a morning of meetings before a scheduled visit to the western Darfur province, where the United States blames his government for recruiting and equipping militiamen to kill rural villagers and burn their homes.
Some rebels wore uniforms provided by the Sudanese Army, US Agency for International Development Administrator Andrew Natsios said on Wednesday.
Al-Bashir denies government involvement, but the US and international organisations say his military sent helicopters to bomb villages before rebels swept in with horses, guns and knives.
Two million people have been
displaced in the Darfur conflict
Prior to her meeting with al-Bashir, Rice said the US was making a difference in relieving a refugee crisis and African peacekeeping troops were helping to stop atrocities.
"We are not where we were a year ago," Rice said on Wednesday, ahead of her first trip to Sudan as secretary of state.
"We are in a different circumstance and the United States has spent a great deal of money and a lot of diplomatic and other energy to try and bring this conflict to a conclusion."
War-induced hunger and disease have killed more than 180,000 people and driven more than 2 million from their homes.
Sudan formed a new reconciliation government this month, following a peace agreement to end a 21-year-year civil war between the Muslim north and the mainly Christian and animist south that killed an estimated 2 million people.
That conflict was separate from the Darfur killings, which began after tribes took up arms in February 2003, complaining of discrimination and oppression by Sudan's Arab-dominated government.
The Sudanese government then allegedly responded by backing a counterinsurgency by militia known as the Janjawid.
Al-Bashir remains in charge of the new government with former southern rebel leader John Garang installed as a new vice-president.
On Tuesday, Garang dissolved his rebel movement and dismissed all government officials in 10 former rebel-controlled southern states.