"We need to work together so that we can have real peace in Darfur," European Commission President Jose Manuel Barroso said as he left the presidential palace in Sudan's capital Khartoum.
"It was very important to understand the point made by the president of Sudan. I also conveyed to him very frankly and very openly our concern about the situation," Barroso added.
International efforts to end more than three years of conflict in Sudan's vast west have intensified in recent weeks.
The African Union peacekeeping mandate in Darfur, which expired on Saturday, was extended to December 31.
The United Nations Security Council has passed a resolution to send 20,000 UN troops to replace the 7,000 AU forces in Darfur.
But Bashir has rejected the mission transfer saying it was a violation of Sudan's sovereignty and an effort by the West to colonise the African oil producing country.
With discussions over the UN troops seemingly at a standstill, some diplomats and aid workers have suggested an alternative to the U.N. force which has been called AU-Plus.
It would amount to an extended AU mission with enhanced policing powers and greater support from the United Nations.
US Secretary of State Condoleezza Rice on Wednesday told Sudan it must choose between "cooperation or confrontation" and accept a UN presence in Darfur.
Barroso did not mention the UN peacekeepers during his brief remarks.
A Sudanese official said pressure should be placed on Darfur rebels to sign a peace agreement.
A peace deal was signed in May by the Sudanese government and one Darfur rebel group, but rejected by other factions and but analysts say violence has increased.
Some 200,000 people have died and more than 2.5 million people have been displaced since rebels in Darfur took up arms in 2003, accusing the Khartoum government of neglect.