"The lesser evil is to come to an agreement with Bashar al-Assad to begin a ceasefire allowing aid to reach the displaced... kickstart a political transition and above all attack our common enemy -- Daesh (Islamic State group)," Jose Manuel Garcia-Margallo told TVE television.
"We have to replace the 'Bashar yes or Bashar no' discourse by one of peace or war. If you want peace, you are going to have get along with Assad at least on a temporary basis."
"(Former US President Franklin D) Roosevelt was forced to come to an agreement with Stalin to finish with the Nazis, as it was a lesser evil at the time."
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Garcia-Margallo said there was still no sign of a concrete European action plan, two days after France used a little-known article in the European Union's Lisbon Treaty rule-book which provides for solidarity in the event a member state is attacked.
France, which has launched new airstrikes against Islamic State militants in Syria, invoked the article after Friday attacks in the French capital left 129 people dead.
"We were surprised as we thought that they would activate another article allowing for mutual aid in case of terrorism," Garcia-Margallo said.
"I think we need to sit down all together and implement a coordinated plan."