Nidal Qatamin told state-run Petra news agency that 15,000 illegal workers, including 5,723 Syrians, were in the kingdom.
"They will be deported starting November 11 unless they obtain required permits and legalise their situations," said Qatamin.
He did not say if the Syrian workers had crossed the border into Jordan among waves of refugees who have fled their country's deadly conflict or if they have arrived there before the war broke out there in March 2011.
Signup to our newsletter and follow us on Facebook and Twitter!
Qatamin added that the decision to expel illegal workers was aimed at helping "provide jobs for Jordanians" and organising the labour market.
Officials in the kingdom say unemployed Jordanians face tough competition from Syrians for jobs.
Unofficial estimates put the number of Syrian workers in the country at around 160,000. The government does not have official figures on the number of Syrians working in the kingdom.
Jordan is hosting around 550,000 Syrian refugees, mostly in the north, including in the Zaatari refugee camp, which is home to more than 130,000 people.
Jordanians have repeatedly called for aid, saying the growing refugee influx has placed a huge burden on already overstretched water and power supplies as well as housing and education.