JK Rowling’s estranged father secretly ran a large-scale marijuana-growing operation from her childhood home in southwest England during the 1990s, while the future “Harry Potter” author was a struggling single mother in Edinburgh, Scotland, a new book claims.

The allegations about Peter Rowling, 81, appear in “A Pen to Change the World,” a new biography by Solomon Schmidt to be released next month.

“When Pete was visiting me at one point in 1997, he told me that over the previous few years, he had been one of the largest growers of marijuana in South West England and Wales,” Peter’s nephew, Ben Rowling claims in the book.

According to an excerpt obtained by The Post, Ben claims his uncle started the illegal operation in the years after the death of JK’s mother, Anne, in 1990 after a ten-year battle with multiple sclerosis (MS).

Ben claims Church Cottage, the family’s former home in Gloucestershire, had a hidden cellar under a trapdoor which led to a sophisticated grow room complete with lighting, ventilation and harvesting systems.

“Pete always had a carpet or rug over the trapdoor entrance, and so you would never know the space even existed unless you lived there or were family,” he said, according to the book.

The book alleges the enterprise ran from roughly 1991 to 1995 and involved a man identified only as “Derek,” who allegedly handled cultivation, packaging and sales.

“After Anne passed away in 1990, Pete vacated Church Cottage and ultimately moved in with his partner, Jan, to a new location,” Ben said.

“The cellar was large, which would have allowed Pete to store a lot of plants down there. It was a perfect place for growing. The brick-and-concrete floor was around two-feet thick, and he had a ventilation system so that nobody would find out,” he adds.

At that time in the UK marijuana cultivation was a serious crime which could have resulted in a hefty prison sentence had police found out.There is no suggestion that JK Rowling was ever aware of Pete Rolling’s alleged activities.

Ben claimed the operation stopped after Church Cottage was sold in 1995, at which point all evidence was supposed to be removed.

“Derek had accidentally left manuals in the attic which detailed how to grow marijuana in the best possible way with the set-up they had used. The female estate agent found these, but nothing more came of it, for a reason unknown to me.”

The marijuana claims in Schmidt’s book have not been independently verified by The Post and Pete Rowling could not be reached for comment. The author said his research led him to believe Peter is incapacitated in his advanced age and in his final days at a nursing home.

Reps for JK Rowling declined to comment for this story.

The allegations add another bizarre chapter to the famously fractured relationship between JK and her father, which the billionaire author has previously discussed publicly.

Peter Rowling was an aircraft engineer at the Rolls Royce factory in Bristol and her mother, Anne, was a science technician in the Chemistry department at Wyedean Comprehensive, where JK went to school.

Anne was diagnosed with multiple sclerosis when JK was a teenager and died before the Harry Potter books were published. JK has one sister, Dianne, who is not a public figure.

Speaking with Britain’s “The Telegraph”, JK previously said she had “never forgiven” her father for his behavior following the death of her mother.

Peter Rowling attended JK’s wedding to Dr. Neil Murray in 2001 in Scotland, but their relationship broke down about two years later.

She has reflected in multiple interviews over the years on a deeply difficult relationship with her dad and revealed they stopped speaking in 2003.

“We’ve not had any communication for years,” she told The Times in 2012.

JK — estimated to be worth $1.2 billion, according to Forbes — said the final straw was Peter auctioning off his Harry Potter first editions at Sotheby’s, according to The Times.

At the time, Peter Rowling said he feared he had lost his daughter after he auctioned the rare books when desperate for cash.

A copy of Harry Potter and the Goblet of Fire, given to him on Father’s Day, 2000, and signed, “Lots of love from your first-born,” went for $48,000, the paper reported.

“It’s a heartbreaking situation,” he said, according to the report in The Times.

“I fear I have lost my daughter. I can only hope Joanne [JK] will one day come to understand why I did it.”

In an interview with the BBC, the renowned writer revealed she had been afraid of her father “for a very long time” and spent years seeking his approval.

“Then there came a point, quite shamingly late in life, when I couldn’t do that any more,” she told the outlet.

While JK Rowling went on to become one of the world’s richest authors after the extraordinary success of the “Harry Potter” franchise, she has spoken openly about living in near poverty as a single mother in Scotland before the books made her a household name.