There have been reports that Rwanda is concerned about Uganda allowing Rwandan dissidents to live and conduct business in the country.
Shortly after presenting her credentials to President Paul Kagame last week, Uganda's High Commissioner to Rwanda Oliver Wonekha, when asked about the reports of bilateral issues between the two countries, said she was not aware of any concerns.
"As far as I know, our relations are good. But you know with a relationship, you must nurture it, you must take care of any gaps that exist. I will make sure that I look at those gaps and attend to them," she said.
Although there has not been any official communication from both countries regarding their relations, a missive circulated after a closed door meeting addressed by Rwanda's Minister General James Kabarebe pointed out key areas which "Rwanda is concerned about".
The EastAfrican has learned that there have been two closed door meetings over the past month of government officials, members of the ruling party and the business community, to provide "an update" on relations between the two countries.
According to an insider, Gen Kabarebe said at the meeting that, "Rwanda is concerned by Uganda's continued offering of its space to 'Rwandan enemies', whether deliberately or inadvertently, to conduct their operations."
"Among other things, Rwandan authorities were worried by the decisions Uganda has taken, which are hostile to Rwanda," the source told The EastAfrican.
"Among them is the decision to allow exiled Rwandan tycoon Tribert Rujugiro to operate in Uganda and work closely with government officials," the source added.
A leaked memorandum of understanding shows a partnership between President Yoweri Museveni's younger brother Gen Salim Sale and Mr Rujigiro, who Rwanda accuses of bankrolling dissidents fighting the government.
The MoU, seen by The EastAfrican, was signed by Gen Saleh and M/S Leaf Tobacco and Commodities Ltd, owned by Mr Rujugiro on June 13, giving the general a 15 per cent stake in the company. In return, Gen Saleh grants "security" to the business.
The MoU came a few months after Mr Rujugiro announced that he would be constructing a $20 million tobacco processing factory in northern Uganda.
Mr Rujugiro, the founder of the PanAfrican Tobacco Group, was a special economic adviser to President Paul Kagame before he fell out with the Rwanda government at the end of 2009 and went into exile.