Former Ontario Liberal premier Dalton McGuinty's chief of staff and deputy chief of staff have been charged with criminal offences over the deletion of computer files related to the gas plant scandal.

The former employees, David Livingston and Laura Miller, are accused by the Ontario Provincial Police of deleting thousands of government emails pertaining to the decision to cancel two Greater Toronto Area gas-fired power plants, in Oakville and Mississauga, in the lead-up to the 2011 provincial election.

The controversial decision will cost Ontario taxpayers up to $1.1 billion, according to the auditor general.

McGuinty's lawyer, Ronald Caza, issued a short statement about the matter saying his client has co-operated with the investigation and is not the target of the OPP investigation.

Dalton McGuinty's former chief of staff and deputy chief of staff are facing criminal charges in the deletion of computer data about 2011's gas plant scandal. (Dave Chidley/The Canadian Press)

"Today's events again confirm there was no wrongdoing on the part of the former premier," Caza said.

The OPP said in a release that the charges come after a "complex" investigation into the scandal led by its anti-rackets branch.

The OPP investigation began in June 2013 after McGuinty's resignation as premier.

OPP Det. Supt. Dave Truax said the investigation took that long because of all the data involved, including more than 13,000 pages of information.

"It involved an interview of a number of persons all over Ontario, Canada and elsewhere," said Truax. "It also involved a thorough forensic review of a ... voluminous amount of electronic data."

McGuinty was questioned about the matter by the OPP in April 2014. Months later, provincial police served a court order to Queen's Park staff asking for documents related to the scandal.

Documents released during the police investigation last February showed Livingston and Miller compiled a list of senior Liberal staffers in the then-premier's office whose computers would be purged.

They then hired Miller's partner, IT consultant Peter Faist, to wipe clean dozens of the hard drives — from within McGuinty's office — on a weekend, the documents alleged. The documents also allege they paid Faist $10,000 to purge 20 hard drives.

Miller resigned as executive director of the B.C. Liberal Party Thursday after the charges were announced.

Confidence in police shaken

Miller issued a statement saying the investigation has shaken her confidence in police and that she has formally complained about some of the OPP investigators involved in the case.

"I have always had trust and confidence in the police," she said. "Today, that is not so."

Later in the statement, she added: "Every Canadian expects and deserves impartiality and fairness in police charging decisions. I do not believe that to be the case here."

The former premier's chief of staff, David Livingston, is charged with breach of trust, mischief in relation to data, and misuse of a computer system to commit the offence of mischief. (Handout)

Miller said she's hired high-profile lawyer Clayton Ruby to defend her. Ruby, in a statement, said: "This is the Office of the Premier of Ontario, for god's sake! No records get destroyed there. They just get stored somewhere else."

Livingston's lawyers said in a statement that they're confident he will be "vindicated" at trial.

"Mr. Livingston did nothing wrong and certainly did not break the law as alleged," said Fredrick Schumann, one of Livingston's lawyers. "He was consistently open about his actions in the premier's office. He always believed that those actions were proper and in accordance with normal practices."

None of the allegations have been proven in court.

Livingston, 63, of Toronto, and Miller, 36, of Vancouver, are each charged with:

Breach of trust.

Mischief in relation to data.

Misuse of a computer system to commit the offence of mischief.

The accused are scheduled to make a first appearance at the Ontario Court of Justice in Toronto on Jan. 27, 2016.

Wynne says government co-operated

Ontario Premier Kathleen Wynne said Thursday that she's aware of the charges, but that the investigation concerns events that took place before she took office.

How many key decision-makers in the Liberal Party need to be charged before Ontario's premier will take responsibility? - Patrick Brown, Ontario PC Leader

"The issues that are before the court concern the former premier and his former staff," Wynne told CBC News.

Wynne said her government has fully co-operated with the OPP investigation. She also added that Queen's Park staff have since been trained about the rules surrounding the retention of government emails and other documents.

Wynne said neither Livingston nor Miller worked in her office.

She added that she wouldn't comment further, as the matter is before the courts.

At Queen's Park, PC MPP Victor Fedeli called the gas plant scandal a "massive coverup," and he said that the government's short-term decision will have caused long-term pain for Ontario families.

Fedeli wouldn't say Wynne knew about the coverup, but he said there's a "shadow" of scandal surrounding the Liberal party.

"This is not a one-off," he said.

NDP MPP Peter Tabuns, who sat on the justice committee looking into the gas plant scandal, said while Wynne may not have known about the deletion of emails, she certainly played a role in the scandal.

Laura Miller, speaking here during her time with the Ontario government, resigned as executive director of the B.C. Liberal Party in the wake of the charges filed against her. (Queen's Park)

'Disgraceful'

Wynne, he said, was at the cabinet table when the Liberal government decided to cancel the gas plants and also stopped the committee's investigation before it had a chance to question Faist.

"I think her hand was very strong in this," he said.

"This government needs to be defeated in its next election."

PC Leader Patrick Brown tweeted that it's "disgraceful" that such high-level Liberals have been charged.

"How many key decision-makers in the Liberal Party need to be charged before Ontario's premier will take responsibility?" he wrote.

NDP Leader Andrea Horwath, meanwhile, tweeted Ontarians are right to be "disappointed" with the government after today's news. Wynne's government, she said, is the "same old government" with the "same ethical problems."