Atkins died last April at age 72 after being injured in a fall on an icy street.
Before his death, he had suffered a heart attack, congestive heart failure and hypertension, The Wall Street Journal reported, citing a report by the city medical examiner.
At 258 pounds, the 6-foot-tall Atkins would have qualified as obese, according to the Centers for Disease Control and Prevention's body-mass index calculator.
Diet is one potential factor in heart disease, but infections also can contribute to it.
Atkins had had a viral infection which had weakened his heart, his widow Veronica said in a statement.
"I have been assured by my husband's physicians that my husband's health problems late in life were completely unrelated to his diet or any diet," she said. "My husband's death resulted from a serious head injury."
Atkins' weight was due to bloating associated with his condition, and he had been much slimmer during most of his life, Stuart Trager, chairman of the Atkins Physicians Council in New York, said.
Atkins' widow blamed "shameless individuals" who violated federal law in obtaining the report. "Obviously such people will have no trouble picking and choosing bits and pieces of fact and supposition to mislead the world."
The medical examiner's report was given to the Journal by the Physicians Committee for Responsible Medicine, a group that advocates vegetarianism.
"If Dr. Atkins himself paid a price for following this sort of diet for a long period of time, that is indeed a tragedy," Dr. Neal Barnard, president of the group, told CBS radio station WBZ-AM.
"The only relevance this would have is if he used himself as an example to show what the diet could do over the long run, and encouraged other people to go on the unhealthy diet that made him a lot of money," Barnard said.
The Physicians Committee maintains the Atkins Diet is unwise.
"Over the long run it is not a good approach to weight control. For some people, it seems to contribute to increased risk of heart problems. We have heard of people dying after following this sort of diet," he said.
In April 2002, Atkins issued a statement saying he was recovering from cardiac arrest related to a heart infection he had suffered from "for a few years." He said it was "in no way related to diet."
On Tuesday, the medical examiner's office would say only that Atkins died of a head injury from the fall.
"I can't comment on people's previous conditions. It's against the law," said spokeswoman Ellen Borakove.
Borakove said that, because of family objections to an autopsy, the medical examiner had conducted only "an external exam" and a review of Atkins' hospital records.
She said a report had been sent to a doctor in Nebraska who requested it, and said he apparently gave it to the Physicians Committee for Responsible Medicine.
It was later discovered that the doctor was not "the treating physician" and should not have had access to the report, Borakove said. The medical examiner's office plans to complain to Nebraska health officials, she said.
Last month, Veronica Atkins demanded an apology from Mayor Michael Bloomberg after Bloomberg called her late husband "fat."