A total of 22 troops flew out of the Torrejon de Ardoz base near Madrid and will replace both the 17 killed in the aircraft that crashed and the five who were injured when a second helicopter made a crash landing nearby.
The ministry also said that investigators were still leaning towards an accident as the cause of the disaster. The most likely hypothesis was that the helicopter, which was on maneouvres, was hit by a powerful gust of wind as it was flying at very low altitude, it said.
There had been unconfirmed reports that the helicopter, which crashed near the city of Herat, had been shot down.
The second aircraft was reported to have made a crash landing after its crew saw the first one go down.
Defence Minister Jose Bono is due to report on the crash before members of the Spanish parliament on Wednesday.