EAC Secretary-General Liberat Mfumukeko says the bloc will "soon" engage the two countries in an effort to seek a solution to the diplomatic and trade dispute.
Mr Mfumukeko blamed the decline in intra-regional trade on political disputes, tariffs and non-tariff barriers to trade.
Businesses in the region have incurred huge losses in the past three weeks following the partial closure of the border crossing between Uganda and Rwanda at Gatuna.
EAC Secretary-General Liberat Mfumukeko said the bloc will "soon" engage the two countries in an effort to seek a solution to the diplomatic and trade dispute that threatens to paralyse cross-border business.
"Our experts are in Rwanda and Uganda on a fact-finding mission, and we will have a report soon. From that report, the EAC will engage the partner states. I cannot give a timeframe, but it will be within the next few days," he told The EastAfrican in Nairobi this past week.
"Our role is to make sure the countries abide by their commitments, and all partner states have signed the Common Market and Customs Union Protocols. We are reminding them that when goods are stuck they are breaching these protocols," he said.
The escalating tensions prompted Kenya's President Uhuru Kenyatta to engage in shuttle diplomacy, On Monday, he travelled to Kigali and held talks with Rwandan president Paul Kagame.
The region's business community is concerned that differences between partner states are increasingly threatening integration at a time when member countries are operating at cross-purposes on trade, amid rising protectionism.
Tanzania has been accused of using NTBs as protectionist measures either through denial of Community tariff treatment, discrimination against other countries' products, charges of equivalent effect and bans of transfer or import of EAC products.
Kenya's exports to the region continue to decline year on year, falling from about $1.3 billion in 2011 to $1.1 billion in 2017.
"The EAC is perhaps the only economic bloc in the world that has been successful in trading globally without learning first to trade with itself. It defies all the promises supposedly offered through regional integration efforts," said Victor Ogola, EABC head of policy.
Mr Mfumukeko said that he hopes that consensus in the review of the bloc's CET will be achieved.
"Technical experts are discussing the different national positions with the aim of combining ideas on how the CET should be reviewed. The proposals will be taken to the Council of Ministers, and eventually there will be consensus," he said.
"At the Secretariat, we are supporting the private sector and we are engaging more. This is because the EAC Treaty establishes that the Community should be market-driven, but the reality on the ground is that many young people are unemployed.