The latest resignation from the North's Human Rights Commission is a "serious development", the Minister for Foreign Affairs has said.
Mr Cowen views the decision of Mr Patrick Yu, a member of the commission since December 2001, to quit with "serious concern".
The commission was set up under the Belfast Agreement and is tasked with advancing the equality agenda in general and working on a Bill of Rights.
Mr Yu resigned on Monday and is the third member to resign in the past year.
The issue has been referred by Mr Cowen to the British-Irish secretariat in Belfast.
Mr Yu wrote to the Northern Secretary, Mr Paul Murphy, claiming he had regrettable been forced to conclude that the commission had adopted a position which undermined aspects of the Belfast Agreement as well as existing human rights protection measures and current equality protections.
In his letter to Mr Murphy, Mr Yu concluded: "There are other issues which have led me to conclude that the commission cannot fulfil its mandate. I believe that I have tried to resolve these difficulties inside the commission but I feel that my efforts have met with very little success."
Commissioners regretted the decision but said they would consider the issues raised.
However, the Council for Ethnic Minorities endorsed Mr Yu's decision.
It said: "We have, for some time, been aware of how hard Patrick has been trying to resolve difficulties from inside the commission.
"Unfortunately, it has become apparent that such efforts have met with little success, particularly in relation to the pursuit of a strong and inclusive Bill of Rights for Northern Ireland."
Mr Cowen said: "I was particularly concerned by Mr Yu's stated grounds of resignation which appear to have troubling implications for specific equality and rights aspects of the Good Friday agreement.
"Taken together with the previous resignations, Mr Yu's departure will undermine vital community confidence in the ability of the Human Rights Commission to protect and advance human rights, a central and critical part of the Good Friday agreement."