The American Society for the Prevention of Cruelty to Animals (ASPCA), which has oversight of the carriage horses, took his body for a necropsy and announced interim findings on October 31.
It said while the cause of death was likely to be inconclusive, the gross necropsy report indicated that Charlie "was not a healthy horse and was likely suffering from pain due to pronounced chronic ulceration of the stomach and a fractured tooth".
Veterinarian Pamela Corey, director of equine veterinary services for the ASPCA's humane law Enforcement department, was reported in the release as saying Charlie was not healthy for a career in an urban carriage horse business.
Dr Corey said in the release: "We are very concerned that Charlie was forced to work in spite of painful maladies, and these particular health issues can be difficult to diagnose because draft horses are by nature a stoic breed, not displaying signs of pain until they are very severe."
However, the Horse and Carriage Association of New York City has highlighted a correction filed by Corey with the Department of Health and Mental Hygiene.
There was no evidence Charlie was suffering from cruelty or neglect, Corey said in what the carriage organisation described as a stunning retraction.
According to Corey's statement, there was no evidence Charlie was in pain during his time as a carriage horse, and by all outward appearances and behaviour, he was healthy.
The October 31 statement from the ASPCA was not supported by the preliminary necropsy report, it said, hence Corey's correction.
"There was no evidence of cruelty or neglect in this case," Corey wrote.
The carriage group said Charlie's death and its "reporting by the ASPCA" prompted widespread outrage in the community.
Demonstrations, threats and slander had been directed against the carriage industry, fueled first and foremost by the press releases issued by the ASPCA and NY-CLASS, which wrongly suggested that his being a carriage horse led to poor health and death.
A spokesperson for the Horse and Carriage Association of New York City, Stephen Malone, said: "Dr Corey's retraction and apology to the industry and to the public corroborates what we in the industry have said all along - that our horses are fit to work and that allegations of cruelty, neglect, or mistreatment resulting from their care in the city are completely unfounded."
He said the assocation was proactive over the health and wellbeing of horses.
It said it also had concerns around issues raised in a report published online in the New York Times, which reported that Corey had been suspended by the ASPCA.
Malone said the ASPCA had a stated goal of banning the carriage business in New York City, but had police powers granted by the state to enforce laws as they pertained to the carriage industry.
He described it as a blatant and longstanding conflict of interest.
Malone said the association would be closely monitoring further developments in the story, and would be making a formal statement soon.
The New York Times report said Corey had taken it upon herself a few days after the ASPCA release to issue a "correction".
It said she had subsequently been suspended in what it described as the latest volley over the contentious subject of carriage-horse welfare in New York City.
The Times said the society declined to discuss why Corey had been suspended but said it had gone back and forth with her over drafts of its original news release about Charlie's death.
It reported Elizabeth Estroff, senior vice president of communications for the ASPCA as saying: "We believe there are no factual differences between our original statement of 10/31/11 and the one Dr Corey asked to issue."
Corey had unsuccessfully urged the ASPCA to release her correction, it was reported.
She was of the view that the original statement implied the carriage driver or other parties dealing with the horse were aware of his condition, when in fact there was "no evidence of cruelty or neglect".
Corey said: "I sincerely want to apologise for the confusion created by these misleading statements."
The ASPCA has countered that nothing in the original statement indicated Charlie's owners were aware of his health problems, and in fact had pointed out the conditions were hard to diagnose because draft horses were by nature a stoic breed, not displaying signs of pain until it was severe.