Responding to what it called misconceptions about caning in the foreign media, especially in the United States, the department told Singapore's Sunday Times that strokes of the cane did however leave bruises and marks.
This is the first time the department has given an account of caning since Fay, 18, was sentenced to six strokes of the cane and four months' jail for spray-painting cars.
Fay is now awaiting a government decision on his plea for clemency. President Bill Clinton has described the caning sentence as excessive.
The Sunday Times said that since Fay was sentenced, foreign media had described caning as barbaric and given their own accounts of caning. It said one newspaper, New York Newsday, ran on 20 April 'an obviously fabricated story of how caning is done here'.
Newsday said Singapore used to hold public canings on a platform outside its main courthouse, adding that Singaporeans loved the sight and would roar as the cane came down on the prisoner's buttocks.
A Prisons Department spokesman said the caning was done in a room and administered by a prisons officer.
Before the caning, the rattan was soaked in water to prevent the cane from splitting and shearing the skin.
'The caning does not cause 'skin and flesh to fly' as alleged by critics. It may, however, leave bruises and marks,' the spokesman said.