Yeyet Oking, the head of Bogor district's immigration office, said the five were deported via Jakarta while another man was released for lack of evidence.
Short-term marriages usually involve Islamic clerics blessing unions between foreigners and local women.
The couples live together briefly before the men return home after materially compensating the women.
The marriages are not recognised by the state.
Oking said that the six men were arrested on Monday during a police raid in Cisarua, a hill resort just southeast of Bogor, after tip-offs from local residents.
The immigration official said that the five deported men were deemed guilty of "not respecting Indonesia's law on marriage and of violating public order."
A detective from Bogor police headquarters, who identified himself as Jeffry said the women were detained by police and would be released after being given "moral guidance" so that they do not repeat their offence.
Vice President Yusuf Kalla recently joked that short-term marriages could be economically beneficial to local women.
His remark provoked public outrage, with parliament member Eva Kusuma Sundari accusing Kalla of promoting legalised prostitution.