Rwanda has condemned Burundi for moving a group of Rwandan Hutus who had crossed their common border, further from the frontier.
Those who fled say Hutus are being persecuted in Rwanda
Rwanda says the Hutus are fugitives from justice, and says the Burundian action amounts to giving them the status of asylum-seekers.
Some 2,000 people have fled to Burundi recently, fearing unfair treatment in new village "gacaca" courts.
The courts were set up to try the huge numbers of people accused of genocide.
Some 800,000 people, minority Tutsis and moderate Hutus were massacred by extremist Hutus in 1994, before a Tutsi-dominated government took control.
"All the Hutus are guilty to them," an angry 45-year-old man named Venuste told AFP news agency from a camp near the border.
"I fled the gacaca," said a woman named Helen, preparing porridge for her three children on a traditional stone oven.
"I was in sixth grade during the genocide. I didn't kill anyone, but the Tutsi survivors accuse me."
"They say anyone older than eight at the time took part in the genocide."
In March, trials opened in more than 12,000 gacaca courts across Rwanda, which had been set up to clear the backlog of genocide-related cases in the overstretched regular judiciary.
The gacaca courts are based on traditional systems of justice, in which the victims confront their alleged attackers in front of other villagers.