The EU official said Brussels had "drawn the lessons from our past experience in Mali in particular and that is why we don't want to have a large-scale EU training mission for Niger".
The official said the mission would involve setting up a centre to help train Niger's troops on "maintenance and logistics issues".
It will also include "specialised training" in areas such as tackling improvised explosive devices and could provide communication and command support for Niamey's military.
The EU is aiming to launch the new mission "in the first months" of next year, the official said.
The 27-nation bloc is revising its footprint in the volatile Sahel region after cutting back its training mission in Mali in response to the deployment of Russian mercenaries to support the ruling junta.
Niger, the world's poorest country according to the UN's development index, is battling two insurgencies that have swept in from its neighbours.
Niamey faces a longstanding Boko Haram campaign on its southeastern border with Nigeria and a seven-year offensive in the southwest which emerged from Mali, where al-Qaeda and Islamic State group jihadists are active.
Following the withdrawal of French forces from Mali this summer, the Niger government fears a security vacuum that could aggravate the situation along the 800-kilometre (500-mile) border they share.
France still fields some 3,000 troops in the Sahel, including 1,700 in Niger.
The EU already has a civilian training mission assisting Niger's police and security services that has been running for a decade.