Huang Jing, a US citizen of Chinese descent who worked at the Lee Kuan Yew School of Public Policy, had his permanent residence status revoked by authorities last week.
His wife Shirley Yang Xiuping, whom the ministry said knew he was acting for a foreign government, was also permanently banned from Singapore.
Authorities did not say which government he was accused of working for but he has written extensively on China and regularly contributed to state-run media.
Huang, who is still in the city-state, confirmed to AFP that he had appealed against the decision to ban him and his wife from Singapore and refused to comment further. Anyone who has their permanent residence status cancelled has the right to appeal.
The Ministry of Home Affairs declined to comment Tuesday.
After news broke last week of the government's decision, the professor told Hong Kong's South China Morning Post the allegations against him were "nonsense".
There were tensions earlier this year when the southern Chinese city of Hong Kong seized nine Singapore armoured troop carriers as they returned to the city-state after conducting military exercises in Taiwan.
Beijing considers self-ruling Taiwan a renegade province awaiting reunification.
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