A dog walker spotted the padlocked pink suitcase at the side of the River Mersey near the Speake and Garston coastal reserve on Tuesday (January 11).
The RSPCA said the dog - a young male - had blood loss from his nose and mouth, which may have been caused by blunt force trauma.
It was believed the body had not been there long before it was discovered as there was "little decomposition".
A search was launched for the dog's owner as they weren't microchipped, however, the name Chantell was written on the side of the suitcase.
RSPCA Inspector Anthony Joynes said: "I am treating this as suspicious as the dog had blood loss from his nose and mouth suggesting a blunt force trauma incident to the head.
"The fact the body was put in a suitcase which was padlocked and thrown into the river is also suspicious.
"Sometimes these injuries can be from road traffic accidents but x-rays have found no broken bones which would be expected - and the way the body was disposed of is clearly unusual."
Anyone with information should call the RSPCA appeals line on 0800 123 8018.
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