David Johnston said his mandate to probe allegations of foreign interference comes from the government and not the House of Commons, after members of Parliament voted in favour of his ouster on Wednesday.
The former governor general released a statement following vote on a motion brought forward by the NDP, which the Conservatives and Bloc Québécois supported while the Liberals stood opposed.
It passed 174 to 150.
It called on Johnston, whom Prime Minister Justin Trudeau named back in March to look into allegations that China tried meddling in the past two federal elections, to "step aside from his role."
It asked the government to instead launch a public inquiry into the issue of foreign interference, a move that all opposition parties want, but that the former governor general recommended against in his initial report last week.
"When I accepted the mandate to act as independent special rapporteur, I did so with full knowledge of the fact that the work ahead would be neither straightforward nor uncontroversial," Johnston said in his statement.
"I deeply respect the right of the House of Commons to express its opinion about my work going forward, but my mandate comes the government. I have a duty to pursue that work until my mandate is completed."
Earlier in the day, Trudeau said he maintained confidence in Johnston, despite the stance of opposition MPs.
Opposition parties initially decried his appointment because of Johnston's family connections to the prime minister's family and the Pierre Elliott Trudeau Foundation.
Trudeau brushed off those concerns, telling reporters that he views the matter as political parties wanting to score "partisan points."
"The fact of the matter is David Johnston has served this country in extraordinary capacities for decades," Trudeau said Wednesday on his way into a meeting with his Liberal caucus.
"He's taken this incredibly seriously."
Government House leader Mark Holland has said he has been trying to negotiate with opposition parties to find additional avenues to address concerns about foreign interference that go beyond what has already been offered.
Holland has repeatedly said the hyper-political rhetoric around the discussions in public has been counterproductive, but he would not elaborate on what else the government is offering.
Johnston said in his report that due to the sensitive nature of national security and the intelligence he studied, there would be no way to divulge the information Canadians are seeking publicly. He said that would defeat the purpose of a public inquiry.
He said what he plans to do instead is hold a series of public hearings to further probe the issue.
Those hearings would focus on hearing from officials of both past and present governments, as well as members of diaspora communities affected by foreign interference attempts.
"Foreign governments are undoubtedly attempting to influence candidates and voters in Canada, and I have identified serious shortcomings in the way intelligence is communicated and processed from security agencies through to government," Johnston said in his statement Wednesday
"As I have indicated, there is much work yet to be done and a further public process is required to identify specific reforms that are necessary to preserve the integrity of our democratic institutions."
NDP Leader Jagmeet Singh had attempted to walk a fine line in promoting his party's motion. He has said that while he has no qualms with Johnston, he understands that others do and that creates an appearance of bias that taints his work.
Conservative Leader Pierre Poilievre has been egging Singh on to trigger an election over the issue.
The NDP signed on to a confidence-and-supply deal with the Liberals, in which it agreed to support the minority government in key parliamentary votes in exchange for movement on shared priorities, such as dental care.
Singh has said he will not kibosh that deal over the issue, arguing that it wouldn't make sense to set the wheels in motion for an election when Canadians have concerns about alleged foreign interference in the last two federal contests.
The motion was brought forward by NDP Jenny Kwan. She recently told reporters that the Canadian Security Intelligence Service informed her she has been a target of China since before the 2019 federal vote, because of her advocacy around human rights in China.
Trudeau has dismissed allegations of Johnston is in a conflict of interest as politically motivated attacks without any basis in fact.
Speaking to reporters last week, Johnston also defended his work, saying this has been the first time his impartiality has been questioned, which he finds "troubling."
He has said his "friendship" with the prime minister is rooted only in the five or so times their families went skiing together decades ago.
Trudeau was also a student at McGill University at the time when Johnston was serving as principal and vice-chancellor.