Kampala has restricted the number of Rwandans it accords refugee status following a request by Rwandan President Paul Kagame to lock out thousands of Rwandans who fled the country for Uganda and Burundi early in the year.
Uganda has rejected at least 1,178 new applications from Rwandans in what the State Minister in-charge of Refugees Christine Aporu described as a "political decision," widely seen as seeking to improve the lukewarm relations between the two countries.
A meeting in Kampala of the Joint Permanent Commission of Uganda and Rwanda, to be held this week, will discuss the issue of the Rwandan asylum seekers, especially their repatriation.
Officials of the Rwanda Repatriation Commission are expected in Kampala on July 18 for a tripartite meeting with Ugandan and United Nations High Commissioner for Refugees (UNHCR) officials.
They will visit the asylum seekers to persuade them to return home.
Kigali says its nationals who fled to Uganda and Burundi were running from justice, as they reportedly fear being called before the gacaca or traditional courts, which are hearing cases related to the 1994 genocide.
In March, trials opened in more 12,000 gacaca courts across Rwanda. The counts were set up to clear the backlog of genocide-related cases in the overstretched regular judiciary.
Ignatius Kamali, Rwanda's ambassador to Kampala, has said if the refugees were indeed fleeing from gacaca, it was right to deny them asylum.
Officials of the Office of the Prime Minister in Uganda, which is in-charge of refugee issues, said that of the 1,262 Rwandans who fled to Uganda in March and April this year, only 84 were granted refugee status.
They said the Refugee Eligibility Committee was not satisfied with the reasons given by 417 families comprising 1,178 individuals.
Dr Richard Sezibera, President Kagame's special envoy to the Great Lakes Region, told The EastAfrican in May that the Rwanda government, had asked Kampala not to grant asylum to its nationals who it said were fleeing from justice. A similar request had been made to Bujumbura.
Uganda's Assistant Commissioner for Refugees, Daudi Kazungu, said last Friday that a decision will this week be made regarding the asylum seekers who are still camped in Nakivale refugee camp in Mbarara district in western Uganda. He said the UNHCR and the Refugee Eligibility Committee had spoken to all the asylum seekers.
"It is up to Uganda to decide how to deal with the unsuccessful applicants," Roberta Russo, spokesperson of the UNHCR in Kampala said last Thursday.
She said that, in many countries, unsuccessful asylum seekers are deported to their homes, but added that Uganda does not normally do this. "There are many Rwandans in Uganda who do not have refugee status but they are not deported," she said.
UNHCR officials said that while Rwandan asylum-seekers stopped streaming into Uganda a month and a half ago, the Rwandan refugees living in the country have now stopped seeking voluntary repatriation. Uganda is home to 14,200 registered Rwandan refugees, some of whom were expelled from Tanzania three years ago while others fled their homes during the 1990-94 civil war and the 1994 genocide. President Kagame has been uneasy about their continued stay in Uganda, saying they are potential recruits for groups opposed to his government.
"The repatriations have stopped because nobody is registering, yet repatriation has to be done on a voluntary basis," said Ms Russo.
"I think because of the situation back at home, which the new arrivals say is not stable, others have been discouraged from returning," she said.
Between 2004 and March this year, UNHCR repatriated 3,050 Uganda-based Rwandan refugees.
Rwanda has in the past charged that opponents of President Kagame's regime were recruiting and training from the Nakivale camp in Uganda, a charge Kampala disputed. Last year, Kigali asked Uganda to ask Rwandan refugees in the country to return home.
Antonio Guterres, the new UNHCR commissioner, in June asked governments receiving large inflows of refugees and asylum-seekers not to kick them out, but instead to abide by the procedures of international refugee law in considering their cases.
"What has happened with the Rwanda refugees in Burundi cannot be repeated," he said, in reference to an agreement between Rwanda and Burundi to send back thousands of Rwandan nationals who sought asylum in Burundi. The UNHCR said it was denied access to those asylum seekers.
Last month, Canada's Foreign Minister Pierre Pettigrew said he was "concerned by the decision of the governments of Burundi and Rwanda to label asylum seekers in both countries as 'illegal immigrants' without due process to determine their status as required under international law."