Correa announced via Twitter the sacking of the heads of the army, navy and air force, as well as joint chiefs boss General Luis Garzon.
Garzon had just told a news conference the funds in question could not be returned because they were dedicated to military pensions.
Correa said the military chiefs had until April to leave office.
The dispute stems from the 2010 sale of 220 hectares that were converted into the Guayaquil park where Pope Francis said Mass during his July visit.
