Foreign Minister Mustafa Osman Ismail telephoned Rice while she was on a plane to a Darfur refugee camp in western Sudan to say he was sorry for what had happened in Khartoum Thursday, a U.S. official said.
"He apologized for the treatment of our delegation and the press corps," State Department spokesman Sean McCormack told journalists traveling with Rice.
Earlier, Rice told journalists on the plane the Sudanese had no right to manhandle them or members of her staff and said it made her "very angry" that she was sitting with Sudanese President Omar el-Bashir when the incident took place.
"They have no right to push and shove," Rice said, adding she had instructed the top U.S. diplomat in Sudan to get an immediate apology from the Sudanese government.
While Rice and el-Bashir were meeting, journalists were taken inside in groups to see the meeting for a photo opportunity. At first, only Sudanese journalists, not those from the United States, were allowed in.
Later, U.S. journalists were allowed access in two separate groups. In the first group, authorities pulled one journalist's microphone out of her tape recorder.
Afterward, Sudanese officials came and apologized to the media. But when a journalist in the second group attempted to ask a question, she was pulled away and authorities intended to kick her out.
CNN's Andrea Koppel said journalists and Rice's staff members were "pushed and pulled" in attempts to keep them out of the meeting.
One of Rice's aides eventually said, "We have a free press in the U.S.," and a Sudanese official responded, "Well, we don't here," Koppel reported.
Rice is visiting Sudan hoping to shore up the country's new government following more than two decades of civil warfare between the largely Islamic north and the mostly Christian and animist south. Sudan's new leaders were sworn in this month.
Rice told CNN that in her meeting with el-Bashir and other officials, she received assurances that it would take steps to halt violence against people, particularly women.
Later in Darfur, Rice met privately with women refugees who have been victimized. Many of the women claim they have been raped by military officials.
It is estimated that up to 300,000 people have been killed and some 2 million have been forced from their homes in a rebellion that has raged in Darfur for more than two years.
The United Nations has accused Sudan of using Arab militias known as Janjaweed to fight the rebels. The Janjaweed are accused of a brutal campaign of raping, killing and looting.
Sudan has admitted arming some militias to quell the rebellion but has denied any links to the Janjaweed and calls them outlaws.