Dr. Anny Sauvageau makes the allegations in a statement of claim filed this week against the government, several high-ranking bureaucrats and the justice minister.
She says her office was pressured in 2014 to top up body transportation contracts with funeral homes by $3 million "to appease the Alberta Funeral Services Association and the rural vote."
Other complaints about funeral homes include that some workers took pictures of crime scenes for personal collections and others told one family it had no choice but to hire their services.
Some funeral companies also double-billed Sauvageau's office and families of deceased persons for transporting the same body, the lawsuit alleges.
Sheila Van Alstyne, president of the Alberta Funeral Services Association, said Thursday the group was made aware of the complaints through the medical examiner's office, but they have never been substantiated. No families have made similar complaints to the association, she said.
Alstyne also said the lawsuit inaccurately portrays an increase in funeral home transportation fees.
Sauvageau claims she brought her concerns last year to justice officials and newly named Premier Jim Prentice. But Prentice told her he wouldn't intervene because she had already filed a complaint with the Public Interest Commissioner, she says.
She also forwarded a list of complaints about funeral homes to the auditor general, she says. That office couldn't confirm if it is looking into the complaints, but a spokesman with the Public Interest Commissioner's office said it has started an investigation.
Sauvageau says in the lawsuit that on Sept. 26, the day after she received a response from Prentice, she was informed her contract would not be renewed. No reasons were given.
Prentice told reporters Thursday that he was told there was a personnel dispute between Sauvageau and the government and that he directed the justice minister to handle it.
The lawsuit alleges the decision not to keep Sauvageau in the position was "in direct retaliation and retribution" for concerns she raised, not specifically about funeral homes, but about political interference.
The independence of the medical examiner's office is essential to protecting the integrity of death investigations, says the lawsuit.
Sauvageau claims she was informed, in private, that her office was not to operate at arm's length and that Maryann Everett, an assistant deputy justice minister, once told her: "Your job is to make the minister look good."
The same woman, the lawsuit alleges, also dismissed Sauvageau's concerns about inflated funeral home contracts with: "You think too much of the taxpayers."
Other allegations of interference include that Sauvageau was forbidden from firing a morgue employee who made a hoax about how another worker was going to show up at work with a gun and kill everyone. She was told the employee might be a relative of a deputy chief of staff of then-premier Dave Hancock.
The lawsuit says Hancock requested a cause of death review in a case after receiving a request from a constituent. Other officials also inappropriately intervened by asking, on behalf of relatives of a legislature member, about another death, says the lawsuit.
None of the allegations has been proven in court and a statement of defence has not been filed.
Justice Minister Jonathan Denis said that it would be inappropriate to comment on a case that's before the courts.