The Bengal tiger used in the Oscar-winning film Life of Pi almost drowned on set in an incident subsequently covered up by the US body charged with ensuring animal safety in Hollywood, according to a new report.

An American Humane Association (AHA) official revealed the near-disaster in an email leaked as part of an extensive Hollywood Reporter investigation into the film industry's treatment of animals.

"Last week we almost fucking killed King in the water tank," wrote monitor Gina Johnson. "This one take with him went really bad and he got lost trying to swim to the side. Damn near drowned." She added: "I think this goes without saying but don't mention it to anyone, especially the office! I have downplayed the fuck out of it."

Johnson's email raises concerns because the AHA is the organisation charged with issuing the coveted "no animals were harmed in the making of this picture" stamp that adorns most Hollywood films. The Hollywood Reporter's investigation alleges officials are too close to the film industry they are supposed to be vetting, and that the label is often unfairly awarded.

According to the report, Life of Pi, which won four Oscars earlier this year, was allowed to continue to use the "no animals" credit despite the fact that the AHA subsequently became aware of the email, and despite allegations that Johnson was engaged in an intimate relationship with one of the film's producers. King was used for scenes in Life of Pi where the CGI version of the Bengal tiger, which is named Richard Parker, was not deemed suitable.

Twentieth Century Fox, the studio behind Life of Pi, denied that King the tiger had come close to death during the production of Ang Lee's 3D spectacular. "The tiger, King, was never harmed and did not 'nearly drown' during the production," a spokesman told the Hollywood Reporter. "We take on-set safety very seriously and take every precaution necessary to ensure that no one – animal or human – is harmed during the production of our films."

The AHA is also alleged to have failed in its duty to protect animals on the set of Peter Jackson's Hobbit trilogy in 2012. Animal handlers, backed by People for the Ethical Treatment of Animals (Peta), at the time accused Jackson's production company of responsibility for the reported deaths of 27 horses, goats, chicken and sheep, mainly because, while not being filmed, the creatures were allegedly kept at a farm filled with bluffs, sinkholes and other "death traps". The AHA said in the wake of the revelations that it only had control of animal safety while filming was taking place.

Jackson and his producers rejected the allegations, saying any incidents "were immediately investigated and appropriate action taken. This includes hundreds of thousands of dollars that were spent on upgrading housing and stable facilities."

The Hollywood Reporter alleged that a number of other incidents on films monitored by the association led to the deaths or injuries of animals. Documents claimed: a husky dog was repeatedly punched in its diaphragm during filming of 2006 Disney adventure movie Eight Below after getting into a fight with another canine; a chipmunk was killed after being dropped during the production of Sarah Jessica Parker comedy Failure to Launch, which was released the same year; and two horses died on the set of children's film Flicka in 2005. The incidents were all ruled to be accidents – in the case of Failure to Launch, the AHA said the incident occurred after filming – and the "no animals were harmed" label was not awarded. But the movies were still able to use the credit "American Humane Association monitored the animal action".

In an ongoing court case brought by Hollywood production co-ordinator Barbara Casey, it is alleged that a horse died during the filming of Steven Spielberg's War Horse, but the fatality was covered up to avoid embarrassment.

According to the Hollywood Reporter, AHA "distorts its film ratings, downplays or fails to publicly acknowledge harmful incidents and sometimes doesn't seriously pursue investigations".

In a statement, the association said it did not recognise the report's findings. "Regrettably, there have even been some deaths, which upset us greatly," the statement read. "But in many of the cases reported, they had nothing to do with the animals' treatment on set, or occurred when the animals were not under our care."

Referring specifically to Casey's War Horse allegation, the AHA said the horse in question died of natural causes "in transit home". It added: "We absolutely and categorically deny the sensationalist, misleading and untrue allegations. We look forward to vigorously defending ourselves through the proper legal channels."

The court hearing is scheduled for March 2014.