Johnston, 19, who is the father of Bristol Palin's son, Tripp, said Palin asked him to keep Bristol's pregnancy "a secret.
"She told me that once Bristol had the baby she and Todd would adopt him. That way, she said, Bristol and I didn't have to worry about anything," Johnston told the magazine in an exclusive interview.
At the time the Palins publicly supported Johnston and Bristol's decision to marry and raise the baby. But now, Johnston, who was paid by Vanity Fair for his work, said he believed that Palin did not want people to know that her then 17-year-old daughter was pregnant.
"Sarah kept mentioning this plan. She was nagging -- she wouldn't give up. She would say, "So, are you gonna let me adopt him?" We both kept telling her we were definitely not going to let her adopt the baby," Johnston said.
Bristol and Johnston called off their engagement soon after Tripp was born, and Johnston's relationship with the Palin family has been strained ever since.
Palin's office did not release a statement, but people close to the former governor pointed out that Johnston has made contradictory statements in the past.
"They always treated me like a son. I mean they were, they were real nice to me. And I thought of her as like my second mother," Johnston told CNN's Larry King in April 2009. "You know, Todd was always, you know, a great guy and helped me out with a lot of things. So I mean they welcomed me."
But in Vanity Fair, Johnston said when the cameras weren't around, Palin paid "no attention to her kids."
"The kids do it all themselves: cook, clean, do the laundry and get ready for school. … Even before the campaign, Bristol was the mom of the house," Johnston said.
Palin told ABC News' Charlie Gibson that she is "a lifetime member of the NRA" and that it is "part of the culture here in Alaska. I've just grown up with that."
But Johnston said otherwise.
"People think that Sarah likes hunting, fishing and camping, but she doesn't," Johnston told the magazine. "I've never seen her touch a fishing pole. She had a gun in her bedroom, and one day she asked me to show her how to shoot it."
Johnston even described tension between Palin and her husband, Todd, saying that they couldn't get through a Hawaiian vacation together without fighting, and there was often talk of divorce.
"They're good on television, but once the cameras would leave they didn't talk to each other," Johnston said. "In all the time Bristol and I were together, I've never seen them sleep in the same bedroom."
Johnston spoke about Palin's decision to resign as governor, saying she often complained that her job was too grueling given the low pay.
"A week or two after she got back, she started talking about how nice it would be to quit and write a book or do a show and make 'triple the money.' It was, to her 'not as hard,'" Johnston told the magazine.
Johnston, a self-described "country guy" who did not want to put himself in front thousands of people on the campaign trail, recently walked the red carpet at the Teen Choice awards and during the Vanity Fair photo shoot admitted he would consider posing for "Playgirl."