"He was found unconscious at the apartment and pronounced dead," the New York Police Department said, adding that pills were found near the body.
Police are reportedly investigating if the Australian actor - nominated for an Oscar for Brokeback Mountain - died of an overdose of prescription pills.
Father Kim Ledger said that the death of his 28-year-old "dearly loved son" had been "tragic" and "accidental".
Speaking in the actor's home town of Perth, in Western Australia, Mr Ledger said that his son had been a "down to earth, generous, kind hearted, life-loving, unselfish individual".
"Heath has touched so many people on so many different levels during his short life that few had the pleasure of truly knowing him."
The actor was found dead in the apartment he had been renting for several months at 1526 (2026 GMT) on Tuesday.
New York police said they did not suspect foul play and that his body had been discovered with prescription pills nearby.
"We are investigating the possibility of an overdose," police spokesman Paul Browne told Reuters news agency. "There were pills within the vicinity of the bed."
The BBC's Matthew Price in New York says the exact cause of death was still being investigated, but suicide has not been ruled out.
Police, journalists and crowds of fans gathered outside the Broome Street apartment in the fashionable SoHo area.
Investigators said Ledger had been due to have a massage at the flat.
The housekeeper went to tell him the masseuse had arrived and found him dead on Tuesday afternoon.
The medical examiner's office said an autopsy would be carried out on Wednesday.
In September the Perth-born actor split from his girlfriend Michelle Williams, with whom he has a two-year-old daughter, Matilda.
Williams played his wife in the 2005 film Brokeback Mountain.
Hollywood stars were quick to offer their tributes and mourn Ledger's death.
"I had such great hope for him," said Oscar-winning actor-director Mel Gibson. "He was just taking off and to lose his life at such a young age is a tragic loss."
In 2001, Mr Gibson had cast Ledger to play his son in the American war of independence epic, The Patriot.
"What a terrible tragedy. My heart goes out to his family," said fellow Australian actress Nicole Kidman.
American actor John Travolta, who was in Australia at the time of Ledger's death, said the young actor had been one of his favourite performers.
"His abilities are rare...it's a tremendous loss," said Mr Travolta.
Brokeback Mountain director Ang Lee said Ledger's performance had been a "miracle" of acting, echoing a young Marlon Brando.
He won an Oscar nomination for his role as a gay cowboy in the film but the award went to Philip Seymour Hoffman for his role as Truman Capote.
Ledger starred in I'm Not There, as one of several actors in a role representing singer Bob Dylan.
He also plays the Joker in yet-to-be-released Batman film, The Dark Knight.
Ledger also starred in A Knight's Tale and The Patriot, and played a suicidal son in Monster's Ball.
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