The controversy was triggered after a soldier filmed a cowering stray dog suspended by a taut white rope around its neck in a military camp bathroom, preventing it from lying down or moving around.
He released it to an animal rights activist, a member of local group Animal Lovers League, who subsequently shared the video on Facebook on January 14.
The 21-second clip displaying the restrained jet-black dog went viral and triggered widespread condemnation from Singapore's animal-lovers.
Singapore maintains a conscript-based military. Every able-bodied male citizen and permanent resident over 18 years must undergo two years of military training.
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In a Facebook post late yesterday the military denied any abuse of stray dogs by the camp's commanders and said the soldier had been punished for violating rules against unauthorised photography inside the camp and disclosure of information to persons outside the Singapore Armed Forces (SAF).
It did not specify the punishment for the soldier but the Straits Times newspaper said he was ordered to be confined in camp for 21 days.
"The SAF does not condone any acts of cruelty to animals... The dogs were never abused. Allegations against these commanders were untrue and unfounded," it said.
The statement however did not comment on how the dog featured in the viral video came to be restrained in the military camp's bathroom.
Animal rights activist Louis Ng said the incident had caused anger as the army statement did not address the case of the dog in the video.
"If you are not going to release all the facts to the public, rumours are going to spread like wildfire," Ng, the chief executive of rights group Animal Concerns Research & Education Society, told AFP.