The EPAs have been viewed as damaging to Africa and rejected by some West African leaders.
However, a compromise is being sought by the EU, the 15-member Economic Community of West African States (Ecowas) and Mauritania.
Mohamed Ibn Chambas, the Ecowas commission president, said at the meeting: "We will be working to harmonise the accords of the middle-income countries to integrate them into a regional framework.
"In the era of globalisation, regional integration remains the only possible way to exist and be a respected actor in world development."
The Ivory Coast and Ghana deals are said to have made an agreement more difficult. They set an immediate abolition of EU tariffs on virtually all exports to the EU and a gradual removal of 80 per cent of imports from Europe over 15 years.
Mamadou Sanou, Burkina Faso's trade minister, said: "The European Commission's decision to negotiate bilaterally causes more problems than it solves."
Sanou said: "If we don't fully assess the implications to bring these bilateral accords back into the regional process, we run the risk of seeing multiple tariff structures, in a way re-nationalising foreign trade policy."
The EU has offered to remove all import tariffs for countries signing EPAs, which they say are the best alternative for current trade preferences given to nearly 80 countries.
The trade preferences are considerered illegal by the World Trade Organisation.
Jose Manuel Barroso, the European Commission president, said in a magazine interview this week: "Our offer is generous and sincere. Much more so than the Americans, Russians or the Chinese. Which continent are African exports going to? Europe. Why all this criticism?"