Reports on Friday put Brexit-bound Britain in the dock for blocking the launch of an EU military headquarters because it opposed any suggestion the unit should have an active operational role.
EU diplomatic sources were quoted as saying the British government was anxious not be wrong-footed on the issue ahead of a June 8 general election dominated by Brexit.
But Johnson said the differences had been overdone and that the problem was about finding the right language, not the principle.
"We understand the vital importance of European countries working together to strengthen our defences," he said as he arrived for an EU foreign ministers meeting in Brussels.
"If they want to come together... with other arrangements, then we don't want to stand in their way. We just (need to) work on the language to make sure that we get it totally right," he said.
In March, all 28 EU member states approved plans for what is known as a Military Planning Conduct and Capability (MPCC) facility in Brussels which would initially coordinate three of the bloc's overseas training operations.
These "non-executive military missions" in Mali, the Central African Republic and Somalia do not involve the use of force.
Diplomatic sources say French and German demands that the subsequent legal text refer to this unit as an "Operational Headquarters" were rebuffed by Britain.
According to a draft text of the conclusions seen by AFP, foreign ministers will agree Monday that the EU "looks forward to the effective establishment, as a short-term objective, of the MPCC".
The MPCC will assume "responsibilities at the strategic level for the operational planning and conduct of the EU's non-executive military missions".
If agreed, this text will go for approval to EU defence ministers who are meeting on Thursday.
EU foreign affairs chief Federica Mogherini, who chairs Monday's meeting, has pushed hard for the EU to take on an increased military role after President Donald Trump cast doubt on the US security commitment to Europe.
Brexit will deprive the bloc of both a nuclear-armed power which wields a UN Security Council veto and a member state which has consistently opposed EU defence integration as a risk to NATO.
Mogherini, top officials and member states led by France and Germany believe that against this backdrop, the European Union must now do much more on defence.
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