"They were then driven across the border to Rwanda, where they arrived the following morning," UNHCR spokesperson Melissa Fleming said on Friday.
Fleming said that two men died during the round-up, after jumping off the trucks which were taking them back to Rwanda. She added that children had been separated from their parents and people with recognised refugee status were amongst those returned.
However, Uganda rejects claims that there was anything wrong with their treatment of the asylum seekers.
“There was no legitimate reasons for them to be given asylum,” said Tarsis Kabwegyere, Uganda’s minister for refugees and disaster preparedness.
He added that Uganda may have to reconsider its strategy for dealing with refugees.
“One of the things that makes Uganda attractive for refugees is that we give them land and Rwanda has a shortage of land. Maybe we have to review that policy, and stop giving land out to everybody. We are running out of space.”
Other non-governmental organisations also take issue with Uganda’s handling of the refugee situation.
“For them to use the police force – 26 people injured, 2 dead – what kind of procedure is that, that they followed,” Dismas Nkunda, of the International Refugee Rights Initiative, told RFI.