The joint deployment will be led by the British and will be part of an overall EU military training mission (EUTM).
Mr Shatter said: “This will be the first occasion there has been a formal joint deployment under the UN mandate of mission involving our defence forces and the UK.”
Mr Shatter confirmed the mission after bilateral talks with Britain’s international security strategy minister Andrew Murrison in Dublin where European defence ministers are holding an informal meeting as part as Ireland’s presidency of the EU.
It will include armed military training as well as human rights issues and the protection of civilians.
Mr Shatter said that the military co-operation, almost two years after the British Queen’s historic visit to Ireland, was a further sign of closer ties between the two nations.
Mr Murrison said: “We discussed today how we can continue strengthening relations between our two countries and our shared interest in supporting the development of Malian forces through an EUTM.
“Discussions are ongoing on the precise make up of the EUTM and a formal decision to launch the mission has yet to be taken, but we envisage that this could be the type of mission where our infantry could work alongside one another.”