MEPs at last week's Strasbourg plenary session voted for a resolution that called on member states to increase EU defence cooperation.
The report wanted to see EU defence-related agencies, such as the European Defence Agency (EDA) and Permanent Structured Cooperation (PESCO), to have the same legal and budgetary status at as the European External Action Service (EEAS).
Parliament's co-rapporteur on the file, Esteban González Pons, said, "This is an ambitious and strategic report that comes at an opportune time, as the security and defence union will be one of the top priorities of the Rome declaration."
The constitutional, legal and institutional implications of a common security and defence policy report was passed by 360 votes to 212, with 48 abstentions.
Co-rapporteur Michael Gahler said, "Member states permanently ignore the fact that the funding of the administrative and operative expenditures for EDA and PESCO from Union budget is the only option under the treaties."
Before the Strasbourg vote, EU defence ministers from all 28 member states agreed to measures to develop closer military defence cooperation, which included establishing a new EU defence HQ in Brussels.
The new Military Planning and Conduct Capability (MPCC) command facility is one of a number of measures put forward by EU foreign policy chief Frederica Mogherini, as part of her paper on an EU global strategy in security and defence.
Mogherini said, "EU foreign and defence ministers […] gave a very clear message: we are progressing steadily towards strengthened defence cooperation and we will continue to do more."
She added, "This is about protecting our citizens. The EU has unique tools to help Europeans to take more responsibility for their security, and to do it more effectively."
The new MPCC will be responsible for planning both civilian emergency operations and EU military training missions, such as those taking place in Somalia, Central Africa and Mali.
Welcoming the decision, Christian Ehler, a Vice-Chair of Parliament's security and defence sub-committee (SEDE), said, "Considering my efforts as first vice chair of the SEDE committee and rapporteur of the Horizon 2020 security research programme report, to establish a joint command and control institutions for civilian and military mission of the EU and its partners, I strongly welcome the decision of the council."
However, ECR group MEP Geoffrey Van Orden questioned the need to expand EU military capabilities since Nato is already providing security for Europe.
"Given the range and intensity of security threats […] in the years ahead, the question should not be what roles can the EU invent for itself, but what are the best means of protecting our nation and their citizens."
However, he accepted that after years of cutting defence budgets, Europe had to adapt to new challenges, such as tensions with Russia and a wave of terrorist attacks.
Van Orden was keen to highlight that Nato already existed to meet these challenges; "We do not need to create duplicate and wasteful new structures in the EU.
"Nato combines the power of the US and Canada with 26 European nations, 22 of which also happen to be EU members. It is the most credible deterrent to our potential enemies and wields enormous operational military strength, the EU does neither."
Instead of pushing "unhelpful military ambitions", he called on the EU to concentrate on soft power foreign policy tools such as humanitarian aid, post-conflict assistance and "stabilisation of failing states".
Sabine Lösing, a Vice-Chair of the SEDE committee, was worried about the lack of political control over these newly formed military structures.
"The establishment of the new headquarters continues the current trend, to improve the military structures of the Union, without addressing democratic control."
She added, "At worst the MPCC might soon be 'upgraded' to lead not only non-executive military missions but everything including full-scale warfare."
Lösing warned, "This is a dangerous step further towards a European army and towards further EU-militarisation."