It appealed to the Transitional Federal Institutions "to engage in an inclusive, meaningful and consensual dialogue involving all sections of Somali society".
Further, "the Council expects the Transitional Federal Institutions to convene the National Reconciliation Congress as soon as possible," it said. "It reiterates its readiness to support the Congress financially and otherwise, provided that the TFG [Transitional Federal Government] will ensure an all inclusive and transparent process."
The Somali government, however, said while help was welcome it was not willing to accept "any conditions".
Information Minister Madobe Nuunow Muhammad told IRIN on Tuesday that the government was perplexed by the EU's attitude. He said the EU had helped the government since its inception in 2004 - the EU is the largest donor to the TFG - "but lately they seem to be putting obstacles in our way".
Muhammad said the EU seemed to have developed an attitude of supporting any opposition to the government.
"The government is curious as to who the EU is fighting," he added.
He said the government was determined to hold a national reconciliation conference that would include "all Somali clans. It is our responsibility to complete the reconciliation process and we will do it.
"We need support. What we don't need and want is any support that has conditions attached to it."
A civil society source, however, welcomed the EU's stand and agreed that "Somalia's problems could only be resolved through dialogue. We have been calling for dialogue involving all Somalis, whatever their political or clan affiliations. I hope the TFG will heed the call of the EU."
The EU council welcomed the talks between the TFG, Ethiopia and the Hawiye [dominant clan in Mogadishu] leadership committee, while condemning the use of force by all sides.
The EU "emphasises that the problems of Somalia can only be solved by political means, building on the Transitional Federal Charter. The EU reiterates the need for a genuine political process, as set out in United Nations Security Council Resolution 1744 (2007)."