The carcasses - in various stages of decomposition - were found lying in the open in bushland outside Bundaberg.
A 71-year-old man and a woman, 64, have been charged with unlawful possession of a firearm.
The woman, who is a licensed greyhound trainer, was also charged with obstructing the police.
The discovery of the body dump on Tuesday came weeks after a scandal erupted over the illegal use of live bait to train Australian greyhounds for racing.
An investigation broadcast by ABC Four Corners in February showed live possums, pigs and rabbits being tied to lures to be chased and killed by dogs at one facility.
A number of trainers have been suspended in Queensland, New South Wales and Victoria, while six Queensland trainers were issued with lifetime bans from the sport.
The chairman of Greyhound Racing Victoria and the entire board of NSW Greyhound Racing also resigned.
Michael Beatty, RSPCA Queensland
"We've always known that there's wastage within the industry, but to find 55 bodies in one spot is a bit disturbing."
Abuse and 'wastage' in Australia's greyhound industry
A spokesman for the RSPCA, which is working alongside police on an investigation in the industry, said the Bundaberg pair were arrested following interviews with others in the industry.
"It was as a result of information given to us that the joint Queensland Police Service and RSPCA investigation team made those arrests," said Michael Beatty.
The pair will appear in court on Friday.
Investigators had gone to the dumping site on Wednesday after a tip-off from a member of the public.
Detective Superintendent Mark Ainsworth told local media the greyhounds appeared to have been dumped over a period of time.
Some appeared to have been shot and shell casings were found at the scene. No attempt had been made to bury the dogs, he said, describing the killings as "nothing short of abhorrent".
Queensland Police Minister Jo-Ann Miller tweeted that she was "sickened" and that animal cruelty would not be tolerated in Queensland.
The head of Racing Queensland, Darren Condon, said his organisation would assist the police and take "the appropriate response".
Australian police have charged two people in connection with the discovery of 55 greyhound carcasses in Queensland earlier this week.