The company announced Fernando Alonso would take over as head of military aircraft at the Airbus Defence and Space unit, replacing Domingo Urena-Raso.
Airbus delivered the first of the turboprop aircraft to France in September 2013, four years late and 6.2 billion euros (USD 7.0 billion) over budget.
Production delays continue to plague the aircraft, which can transport up to 37 tonnes including armour or helicopters over a distance of 3,300 kilometres (2,000 miles) to land on unprepared terrain such as sand.
Britain has ordered 22 of the aircraft.
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Airbus also shifted responsibility for industrial-related activities concerning the A400M to its operations group, with development and customer deliveries remaining under the scope of the military aircraft business unit.
"These organisational changes are designed to allow more efficient operations inside the Airbus Defence and Space Division and to put the A400M programme as well as its industrialisation in a position to best address currently existing shortfalls," said Airbus in a statement.
The shakeup comes after Germany's defence minister sharply criticised Airbus at the weekend, saying the A400M delays were affecting the country's ability to be a reliable partner in NATO.
Germany received in December, four years late, the first of the 53 A400M aircraft it has ordered. However Der Spiegel weekly reported the German military has found 875 failings in the aircraft including missing insulation on wiring.