Rwanda says more than 200 of its citizens are being illegally detained in Uganda.
Delegations from the two neighbouring countries have been holding discussions in the Rwandan capital, Kigali, to work towards resolving political and security tensions.
The meeting followed an agreement signed by the two countries’ presidents in Angola a month ago.
Uganda has agreed to review the list of alleged detainees, provide due process, and release those who are found to have committed no crime.
Relations between the two countries have been strained at different times over the past two decades, according to BBC Africa report.
The latest spat has lasted for most of this year and led to Rwanda closing its side of the common border in February.
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One of the problems has been accusations by Rwanda that Uganda is holding hundreds of its citizens illegally, as well as sheltering dissidents, the BBC Africa report stated.
Uganda has also accused Rwanda of training and deploying spies to its territory.
The delegations from both countries agreed to discuss the issue of free movement of people and goods at their next meeting in the Ugandan capital, Kampala in a month, an indication that the border may remain closed for the time being.
The two East African countries are closely interlinked, and there is a considerable population of Rwandan descent in Uganda.