Lack of funds threatens the functional capacity of the Economic Community for the Great Lakes (CEPGL), according to a senatorial foreign relations committee report.
CEPGL brings together Rwanda, Burundi and Democratic Republic of Congo (DRC).
"Only Rwanda is making good of her annual contributions," the 14 page report reads in part.
The report reveals that up to 2011, outstanding amounts owed to the secretariat amount to Euro 3.18 million.
DR Congo tops the arrears list with Euro 1.4m, Burundi second with Euro 1.3m and Rwanda with Euro 0.48m.
The chairperson of the senatorial foreign relations committee, Senator Jean Damascene Bizimana, however informed the Upper Chamber of Parliament that Rwanda had fully cleared its debts.
"Foreign affairs officials said Rwanda has already cleared its debt [Euro 0.48m]," he said.
The report indicates that whereas the secretariat's budget estimates for 2011 were Euro 2.3 million, only Euro 1.3 million was realised. This translates to a mere 55.2 percent.
Other contributors to the budget were the European Union, French Co-operation, UN Women and rental fees accruing from CEPGL's assets.
"We should congratulate the government for not being in debt. It's an indication of support," vice president of the Senate, Bernard Makuza, said while contributing to the debate.
Senator Bizimana told the upper house that the secretariat lacked political direction since no Heads of State summit has been held since the bloc was revived in 2007.
"The Council of Ministers has not convened for years...this has greatly hampered the progress of the activities of secretariat," the report says.
The committee applauded the CEPGL Secretariat for conducting a youth camp comprising of members from the three countries who advocated for peace building.
In 2010, CEPGL member states agreed to increase border operation hours to boost trade.
However, last month, DR Congo authorities cut down on operation hours at its entry points with Rwanda, which has had adverse effects on cross-border trade.
On the fateful day alone, close to 500 travellers were stranded at two border posts, after the DRC government abruptly shut down their border operations earlier than usual.
Most of those stranded were long distance traders who use Rwanda as transit to the DRC as well as traders who operate across the border towns of the two countries.
CEPGL was created in 1976 to fast track economic integration of the three neighbouring countries.