Australian media had reported that Ashley Dyball was detained in Germany after travelling to Europe for a break from working with a Kurdish militia group known as YPG.
"We are aware Mr. Dyball was detained by German authorities in Berlin," a spokeswoman for the Department of Foreign Affairs and Trade told AFP via email.
"We understand a German court has ruled that Mr. Dyball will be deported to Australia."
The ministry gave no indication of any charges against him.
Australian officials have been increasingly concerned about citizens travelling to Iraq and Syria to join extremist groups such as Islamic State (also known as Daesh), with some 110 Australians currently fighting in the region. As many as 45 have died in the conflict.
Canberra has introduced new laws to combat the threat, with foreign incursions offences updated as part of new counter-terrorism laws introduced last year aimed at blocking jihadists going overseas to fight.
Under the laws, it is a crime to fight for militants on either side of the conflict.
The Australian foreign ministry gave no further details on Dyball's case, beyond saying he was being given consular assistance and they were working with German authorities.
"As is our long-standing practice, the government will not discuss specific law enforcement or intelligence matters," the spokeswoman said.
Dyball's family, who previously travelled to Syria to attempt to persuade him to come home, have also urged him to return to Australia.
"It is time for you to return home Ashley," the family said in a statement to the Australian Broadcasting Corporation via a spokesman.
"Please do not fight the deportation back to Australia," the statement said, adding that the matter needed to be resolved in Australia and "not on foreign soil".
"It is time to clear your name as you have done nothing wrong," it said.
Speaking to the "60 Minutes" television programme in Syria earlier this year, Dyball said he was carrying out humanitarian work in Syria and clearing land mines.
"We're here for humanitarian aid," he said.
Dyball is not the first Australian to travel to Syria to work against the Islamic State group.
Reece Harding, 23, died in June in Syria after stepping on a landmine while fighting the militant group alongside Kurds.