BEHIND closed doors, a furious Tom Cruise is at the center of two explosive scandals that could blow the lid off his private life, The National ENQUIRER has learned.

While the Hollywood megastar has long insisted that he is not homosexual, nightmare rumors – said to be about the 52-year-old father of three – about his sexuality have made it into print. The incredible claims and outrageous allegations involve same sex love affairs, and appear in author Amy Sohn’s blockbuster book “The Actress,” which its publisher has promoted as a “big, juicy literary novel.”

But The ENQUIRER can reveal that “The New York Times” and other websites have labeled the book a “roman a clef” – a novel about real people clothed as fiction – and they claim its main character is three-times divorced Cruise! In “The Actress,” Sohn offers a thinly veiled version of Cruise’s life, complete with sham marriages and “fake looking relationships with women,” say reports. Now sources close to Cruise have told of the Hollywood icon’s secret anguish at the sex slurs.

Privately, he is blasting the latest lies and false claims that threaten to taint his straight-arrow image. “Tom is fit to be tied!” said an insider. “He is upset when fabricated stories about him are published as if they were the truth. He’s also upset that this novel suggests he is leading a closeted homosexual life.”

Referring to the novel’s main character in its July 7 review, “The New York Times” said “obviously he is modeled on Mr. Cruise.” But the article also pointed out that the character, unlike Cruise, isn’t associated with the controversial religion Scientology. The character “has no religious affiliation with a famously litigious church that might go after the author or publisher,” the review noted. An insider added: “Tom must be beside himself over this book. It dredges up all the old gay rumors once again. This is a headache that will simply not go away!”

Adding to the big-screen icon’s woes, a lawsuit involving his former Scientology auditor and the church’s legal affairs adviser, Marty Rathbun, could reveal even more secrets, said the source. The suit is set to be heard by a judge in Texas, and was filed against Scientology by Rathbun’s wife, Monique.

In it, Rathbun claims she was harassed and even followed to work. Tom with Church of Scientology leader, David Miscavige Chad Slater made false statements about the actor’s sexuality

“Marty previously claimed that Scientology spied on the actor’s every move,” added the insider. “If Tom is called to testify in the case, he could face some serious questioning about his private life – and it could settle the issue of whether or not Tom is gay.”

Marty Rathbun was a Scientologist for 27 years. At one point, his title was “Inspector General of the Religious Technologies Center.”

Before leaving the church in 2004, Rathbun, 57, conducted “audits” – a form of Scientology counseling – with a slew of celebrity members, including Cruise.

In an interview with London’s “Independent,” Rathbun said Tom invited him to L.A. for auditing sessions in 2001 while the actor was divorcing his second wife, Nicole Kidman. At the time, the “Top Gun” star was also battling gay porn actor Chad Slater over outrageous, false statements about his sexuality. Cruise – who vigorously pursues those who question his sexual orientation – took on Slater after the hunk was quoted in a French magazine as saying he had an affair with Cruise. Slater later recanted.

Experts say it’s possible information about Cruise’s private life could be divulged during testimo- ny in Monique’s court case. Top attorney Alison Triessl, who is not involved in the suit but studied it for The ENQUIRER, said: “Any conversation they (Rathbun and Cruise) had during the course of their friendship outside of the auditing process, regardless of how personal they may have been, may very well come out at trial.” Another former Scientologist agreed that Tom has plenty to fear if Rathbun testifies.

“As Tom’s auditor, Marty knows everything about him. Nothing is hidden,” Margery Wakefield, who wrote the book “Testimony” about her Scientology experience, told The ENQUIRER. Scientology may also have maintained a secret file on Cruise, said a source.

As The ENQUIRER reported in August 2013, a Scientology staffer reportedly provided Scientology leader David Miscavige with detailed, daily reports about the Cruise household for years, former officials said. Later, Cruise – without his knowledge or consent – was reportedly secretly videotaped via hidden cameras during his “auditing sessions.” The ENQUIRER also reported that ex Katie Holmes was also audited, according to sources, and the church has those tapes as well. Those tapes were also personally delivered to Miscavige, according to former Scientologist Claire Headley.

“David seemed to know everything,” the source added. “And some of those secrets have the possibility of emerging in the Rathbun lawsuit.”

‘WE NEVER DISCLOSE SECRETS’- CHURCH OF SCIENTOLOGY Responds — A lawyer for the Church of Scientology has blasted Rathbun to The National ENQUIRER in the past, saying he has “pursued his personal vendetta against” the church for years, “making numerous false, defamatory statements.” The lawyer also charged that Rathbun admitted he perjured himself in a court case involving Scientology. Reps from the church pointed out that auditors are Scientology ministers who “have a duty to keep such communications secret, much like a Roman Catholic priest has a religious obligation not to divulge the contents of confessions.” In the past, a church rep has also told The ENQUIRER: “The church treats the secrets of parishioners imparted to it as sacrosanct. It never discloses them.” The church has also previously denied that it audiotaped or videotaped subjects without their consent. Nor does the church keep “secret files” on its members.