"We have already deployed 2,000 personnel," Santoso told journalists on the sidelines of a meeting of retired officers here.
The first contingent of soldiers was deployed about one hour after the earthquake struck on Saturday, he said.
Army personnel would be deployed for an initial period of one week, he said, but added that their assignment could be extended if necessary.
More than 5,400 people were killed and thousands more injured in Saturday's powerful quake, according to the latest official toll.
Indonesian soldiers would help to evacuate victims requiring medical attention, direct clean-up operations, transport medical equipment and help with the distribution of food aid.
The army has set up one field hospital in hard-hit Bantul district and will help prepare hospitals in at least three other cities -- Magelang, Purwokerto and Semarang -- to relieve pressure on overcrowded facilities in Yogyakarta, Santoso said.