The deteriorating ties between Rwanda and Uganda could deal a major blow to regional projects.
Observers say that if diplomatic ties between the two countries worsened further it could hamper planned Central Corridor infrastructure projects.
The widely reported tension adds to an already delicate situation where some of the bloc members are currently not on talking terms.
Kampala and Kigali remain tight-lipped on what could be the thorny issues but officials have confirmed that Kigali is rattled by several decisions made by Uganda, including arrests of senior police officers suspected of working with Rwandan authorities.
Efforts to get a comment from the Minister for Foreign Affairs and Co-operation Louise Mushikiwabo were futile, while the State Minister in charge of EAC Affairs, Olivier Nduhungirehe said the issues were being handled through “appropriate channels.”
“It’s a sensitive issue that we are dealing with through appropriate channels,” Mr Nduhungirehe said.
The EastAfrican has obtained reliable information that different interest groups continue to be “briefed about the situation” between the two countries, urging them to exercise caution when travelling to or conducting business in Uganda.
Simmering tensions are beginning to affect movement of people between the two neighbours, with Uganda officials reportedly scrutinising Rwandans crossing over to Uganda. Observers say if the developments are anything to go by, regional integration could be dealt a heavy blow.
“If what is being reported in the media is correct, then we are likely to see what is happening have a negative impact, not only on the friendly relations between Rwanda and Uganda but also the EAC in general,” said Dr Christopher Kayumba, a senior lecturer and commentator on regional matters.
He said that whenever such developments happen, free movement of people and trade are affected while regional integration projects are set back.
“It is not only Uganda and Rwanda. If you see what is happening between Kenya and Tanzania and also Rwanda and Burundi, you realise that the signs are not good for regional integration, if cows and chicken cannot move freely,” said Dr Kayumba.