The Malian government in January called in military support from former colonial power France to help take on nomadic Tuareg rebels and al-Qaida fighters who seized territory following a coup in early 2012.
The United Nations announced last week the Malian government brokered a truce with Tuareg rebels during negotiations in neighboring Burkina Faso.
Foreign policy chief for the European Union Catherine Ashton described the agreement as historic. The European and French governments last month hosted a donors conference for Mali with the aim of financing the country's political reforms.
A statement Monday from the Council of the European Union said the deal brokered with "non-terrorist groups in northern Mali" was a positive development. The council described the deal as an "important step" toward successful elections in July and the restoration of Mali's territorial integrity.
Anti-government forces in Mali are accused of war crimes. The United Nations said armed groups operating in northern Mali are suspected of recruiting children.
Elections are scheduled July 28.