A council worker made the discovery while emptying bins in Peebles in the Scottish Borders.
They were found in the East Station car park on Edinburgh Road and it is thought they were put there at some point between 8.30am on Wednesday and the same time yesterday, police said.
The puppies - two of which were male and one female - are believed to be a breed of terrier or terrier-cross.
Two were mixed black and tan and one was more prominently black.
It is not known if they were alive or dead when placed in the bin.
Officers are now urging anyone who saw anything suspicious in the area to get in touch.
Police Constable Nicola Robb said: “This was a horrible discovery for the council worker.
“We are working with the Scottish SPCA to investigate and urge anyone who has any information that can help us trace the individual responsible to please get in touch.”
Jenny Scott, Scottish SPCA senior inspector, said: “At this stage we do not know how these puppies died or whether or not they were alive when they were put into the bin.
“We would appeal to anyone with information about this incident to come forward.”