The decision was announced by government spokesman Steffen Seibert during a news conference on Wednesday evening.
"Sending people back on commercial airlines takes priority but if there is insufficient capacity then… we will consider making use of military aircraft," Seibert said.
The move comes amid Germany's efforts to cope with an influx of about 10,000 migrants a day, with at least 800,000 asylum expected in the country this year.
Commenting on Germany's mounting number of migrants, Chancellor Angela Merkel said earlier this week that "if (economic grounds) is the only reason for being here, then we will have to say more strongly to these people: you must go home."
The German Interior Ministry said in turn that by the end of September, around 193,000 people were registered in the country as having no valid reason to claim asylum. They included more than 140,000 migrants who were granted "exceptional leave to stay," according to the ministry.