Tanzania’s decision to expel about 20,000 Rwandans could worsen relations between the two countries that were already soured following a call by President Jakaya Kikwete for Kigali to hold talks with a group linked to the 1994 genocide.

Some 1,006 Rwandans, mainly pastoralists who were living in Ngara district, Kagera Region in the northwest of Tanzania, have already crossed into Rwanda following the expiry of a two-week July 29 ultimatum issued by the Tanzania president.

The head of state had said the Rwandans were living in Tanzania illegally, and given instructions to local authorities and the Tanzania People’s Defence Forces (TPDF) to expel all immigrants of Rwandan origin.

The Rwandans had sought refuge in Uganda in 1959 during the first genocide.

While President Kikwete did not link his action to the outrage that greeted his May 26 remark urging Rwanda to seek talks with the eastern DR Congo rebel group, the Democratic Forces for the Liberation of Rwanda (FDLR) — made up mostly of remnants of the Interahamwe militias that carried out the 1994 genocide in Rwanda — the expulsion is being interpreted in this context.

(Read: Unease in Kigali over Kikwete’s call for talks with FDLR)

Foreign Minister Louise Mushikiwabo avoided dwelling on the issue, only saying the decision was “unfortunate and regrettable.” She said Rwanda was ready to welcome its people and resettle them.

A Rwandan official said governors from the affected area in both countries were already working on repatriation arrangements for the group, “known to both sides as undocumented immigrants.”

“The unfortunate thing is that many of them are coming back without their property, including their animals. We would like the Tanzanians to ensure the safety of these people,” said the official.

This is not the first time Tanzania has expelled people of Rwandan origin from its soil. In 2000 and 2006, thousands of people were expelled, triggering a massive human and animal movement.

Rwanda faces a serious shortage of land and at the time of going to press, the Ministry of Disaster Management and Refugee Affairs was said to be struggling to resettle the fleeing people with hundreds of cattle.

Relations between Rwanda and Tanzania have soured since President Kikwete made his controversial remarks on the FDLR, with President Paul Kagame accusing Tanzania of sympathising with a genocidal force that has for the past 19 years been operating from the jungles of eastern DRC.

In an address to the nation two weeks ago, President Kikwete admitted that relations between Tanzania and Rwanda had “soured,” but said it was not in the interest of Tanzania to escalate the situation.

He said his government was open to talks with Rwanda to resolve the impasse.

While both countries are playing down the possibility of a diplomatic fallout, neither of the presidents nor their ministers has sought out the other for direct talks.

Rwanda’s Louise Mushikiwabo insisted Thursday that relations with Tanzania were intact but was quick to add that Rwanda did not take “lightly” anyone who looked at FDLR as “just an enemy” to talk to, explaining that such a suggestion condoned the crime of genocide.

Ms Mushikiwabo said while Rwanda and Tanzania have no choice as neighbours but to live together, President Kikwete’s remarks remained “a major concern.”

“The issue of the genocidal force known as FDLR is an issue that is of importance to Rwanda. It should be an issue of importance not only to our neighbours but the whole world because it is an armed group that has a military presence in DRC.”

“When you are associated with genocide, you should be the enemy of everybody. Therefore don’t expect the FDLR to be described as the enemy of Rwanda, it should be the enemy of the whole world,” Ms Mushikiwabo had said the first time the government of Rwanda reacted to President Kikwete’s remarks.

Ms Mushikiwabo said Rwanda’s policy towards the FDLR remains unchanged: Put down your weapons, set aside the extermination agenda and come home.

“That policy is not about to change. There is no conceivable way this country would sit around the table with people who are accused and are associated with the genocide,” she added.

There have been calls on Rwanda supporting President Kikwete’s suggestion, including the United Nations Secretary General Ban Ki-moon who urged Kigali to find ways of addressing the 19-year standoff between the current government and the Hutu rebels.

Several theories have been advanced, with some suggesting that FDLR has been weakened and poses no threat to Rwanda even though other reports say the rebel force has been reinforced and could be 6,000-strong.

Intelligence reports indicate that FDLR could be planning fresh attacks on Rwanda.