A plane carrying a third group of at least 18 Afghan asylum-seekers rejected by Germany left for Kabul late on February 22.
Police said around 250 people gathered at the airport to protest the deportations, which German opposition parties and rights groups have criticized, arguing that most of Afghanistan is not safe for return.
"There are no secure areas in Afghanistan," said Nadine Kriebel of the Bavarian Refugees' Council, which organized the rally. "We want to lodge a protest against these indiscriminate deportations."
In the past, the majority of Afghans whose asylum bids were declined were allowed to remain in Germany due to the security threat in their country. But Berlin, which participates in NATO forces in Afghanistan, decided last year to designate parts of the country safe for return.
The government said the group deportations are supposed to send a signal to Afghans that Germany only accepts a small number of asylum bids from their country.
Peter Altmaier, German Chancellor Angela Merkel's chief of staff, defended the deportations on Deutschlandfunk radio.
"Those who have no claim to asylum from any conceivable point of view - where the courts have determined that they do not face the threat of persecution - must expect to be repatriated," he said.