Monegan says that he also met with Todd Palin in the governor's office in January 2007 and claims, "He showed me ... private investigator reports, letters, correspondence" that raised issues suggesting Wooten should be punished.
But Monegan says when he brought the information back to his office and compared it to the commission's internal file on Wooten, which contained complaints filed by Palin's sister, he says he didn't find anything new.
Monegan says Wooten had already been disciplined by his predecessor for the same complaints raised by Palin and her husband.
"They were already done deals and he had already been punished," says Monegan, who adds that the governor called him late at night on his cellphone a few days after his meeting with Todd Palin.
"There was no new evidence, and I called [Todd Palin] back and told him it was a closed case," Monegan says. "He wasn't happy to hear that. I got a subsequent phone call from the governor about it, and she wasn't happy, either."
In total, Monegan says he and his office received 24 calls over 17 months from the governor, her husband and her staff about Wooten.
Monegan suspects Todd Palin was tracking Wooten's activities because Monegan says the governor's husband once called to complain that the trooper, who was on light duty because of an injury, was snow-machining at his residence far from Palin's home.
Monegan declined to discuss details of Wooten's alleged misdeeds, citing the ongoing investigation and Monegan's upcoming Sept. 10 interview with Branchflower, the independent investigator hired by the state senate's Legislative Counsel Committee.
On July 11, Monegan says he was called to the governor's office where chief of staff Mike Nizich told him he was being removed from his position because Palin wanted to take the Department of Public Safety in a different direction.
Monegan is convinced that his refusal to discipline Wooten was a major factor in his dismissal. He says he understands Palin's passion about the issue.
"I've been a cop for a long time, and I know how emotional divorces can get," Monegan says. "If, in fact, it turns out to be the case [that the investigation determines that Palin abused her office by exerting pressure], she's just being human."
The alleged meetings with Monegan may have been just the latest steps in Palin's apparent campaign to alert Wooten's superiors to his alleged misbehavior.
In 2005, less than three months before she began her campaign for governor, Palin sent an e-mail from her personal account to the head of the Alaska state troopers about Wooten. The e-mail was obtained by ABC News and other outlets.
In the message, Palin relayed more than two dozen incidents in which she or others alleged Wooten had driven drunk, made threats, violated game hunting laws, hurt his son, abused his authority as a law enforcement officer, been unfaithful to his wife, and more.
Palin noted allegations that Wooten had threatened to "bring Sarah Palin down," as well as make Palin's father "eat a f******* lead bullet."
The allegations, taken together, "would lead a rational person to believe there is a problem inside the [state troopers'] organization," asserted Palin in the e-mail.
"I have objectively separated the divorce and Wooten's threats against me and my family with the fact that the troopers have a loose cannon on their hands," Palin wrote.
Justin Rood also contributed to this story