Justin Trudeau has often said that open party nominations would allow local members to choose who can become a Liberal candidate, but a recent race shows that the Prime Minister has the final word over who gets on the ballot in some of these hotly contested campaigns.

The Globe and Mail has learned that Mr. Trudeau played a key role in blocking the candidacy of a local power broker ahead of the nomination meeting in the Montreal riding of St-Laurent last week. After an investigation, the Liberal Party's Green Light committee, which vets candidates in nomination races, rejected Alan DeSousa, the long-time mayor of the borough of St-Laurent.

Related: Liberal Party says it has full discretion to vet candidates in local races

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The matter was then brought to Mr. Trudeau. The Liberal Leader was briefed on the committee's rationale and approved the decision to block the candidacy, a senior official confirmed.

The official said there was not a single reason that explained the "red-lighting" of Mr. DeSousa's candidacy. Instead, the Liberal Party and Mr. Trudeau made a subjective assessment in relation to Mr. DeSousa and whether he was the right person to become the face of the party in St-Laurent, the official said.

The Liberal Party, however, has refused to provide any explanation for its decision to the public, or even to Mr. DeSousa. The move has reignited concerns among Liberal candidates and their supporters about the state of internal democracy in the party. Holding open nominations – instead of directly appointing candidates – has been a key element of Mr. Trudeau's efforts to attract fresh blood to the party since his election as Liberal Leader in 2013.

The public battles between Liberals reinforced the sense that candidates had to work hard for a place on the ballot, in the same way Mr. Trudeau himself ran for the nomination in the Montreal riding of Papineau in 2007.

However, the process has been publicly decried as opaque and arbitrary by some party members who argue the Liberals are willing to bend party rules or impose decisions to influence the outcome in favour of preferred candidates.

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The list of nomination meetings that have been mired in controversy is long, starting with the one ahead of the Trinity-Spadina by-election in 2014. The matter haunts the Liberals to this day, as would-be candidate Christine Innes is suing the party over her exclusion ahead of the vote.

Other races that have been marred by division and infighting in recent years include the ones that were won by former Toronto police chief Bill Blair and Heritage Minister Mélanie Joly. They both benefited from high-level endorsements, which irked other candidates already in the race.

In one bitter fight in 2014, in the riding of Mississauga-Lakeshore, the losing campaign of Julie Desjardins has long alleged irregularities on the part of the eventual winner, now Liberal MP Sven Spengemann.

One of Ms. Desjardins's supporters, former Liberal MP Paul Szabo, has conducted a long investigation into the expenses of the team of Mr. Spengemann, who has since acknowledged making an excess contribution of more than $2,000 to the campaign. Some of these funds were used to cover a printing contract that had originally been paid by Jamie Kippen, who now works in Mr. Trudeau's office, but wasn't initially reported to Elections Canada, records show.

Mr. Szabo alleges that he uncovered a series of questionable tactics during the nomination, such as bulk purchase of the membership cards that gave residents a chance to vote, even if they didn't pay the required $10. The Liberal Party has acknowledged that it recently paid back $50 to the Receiver-General of Canada – or the equivalent of five membership cards paid with other people's money – as a result of Mr. Szabo's investigation.

In an interview, Mr. Szabo pointed out that Ms. Desjardins lost her nomination by fewer than 20 votes, arguing irregularities in the process could explain her defeat. He said that when candidates fail to gain favour with the leadership of the party, "they have many ways to zap you."

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Former Liberal MP Marlene Jennings was hired by the Liberal Party ahead of the 2015 general election to handle complaints from various nomination contestants. Along with co-ombudsman Andy Mitchell, who is also a former Liberal MP, Ms. Jennings sent a report to Liberal President Anna Gainey that stated nominations were flawed.

"I thought the process needed to be modified to be more transparent and fairer, which is how I feel to this day," Ms. Jennings said in an interview. She added that the recommendations to open up the Green Light process were not followed, stating the Liberal Party "wants complete control over who will be a candidate and who won't."

Of the five ongoing by-elections across Canada, two have featured bitter nomination battles.

In Markham-Thornhill, which was vacated by former immigration minister John McCallum in January, only about 200 members voted after the party imposed a retroactive cutoff date for new members. Candidate Juanita Nathan dropped out of the race after saying 1,600 new members had been declared ineligible to vote. The race was won by Mary Ng, a former director of appointments in Mr. Trudeau's office.

In the multiethnic riding of St-Laurent, which was vacated by former Liberal leader Stéphane Dion, Mr. DeSousa speculated he was pushed aside to make room for Yolande James, a former provincial minister with strong allies in the Liberal hierarchy.

Ms. James lost in the first round of the vote. The final result shocked many Liberal Party members as 26-year-old teacher Emmanuella Lambropoulos won in the second round against fiscal law professor Marwah Rizqy.

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Still, Mr. DeSousa argues the result was actually a backlash against the meddling of the Liberal Party in the race. Ms. Lambropoulos was the only one of the three candidates who lived in St-Laurent.

"The machinations and shenanigans that were used to take away my opportunity to be on the ballot may have worked in the 1950s, but not in 2017," Mr. DeSousa said.

Mr. DeSousa said he provided the Liberal Party with a police report and financial data to show he was "clean as a whistle." He acknowledges he was likely hurt by the fact Montreal municipal politics were broadly tainted in recent years by a number of collusion and corruption scandals. In 2013, Quebec's anti-corruption unit raided a number of municipal offices in Montreal, including the one in the borough of St-Laurent.

However, he insisted he has never been under investigation.

Mr. Trudeau has continued to defend his party's nomination policy throughout recent controversies, suggesting complaints came from those who "speculate and create conflicts."

In coming months, he will have to decide how to proceed ahead of the 2019 general election. One possibility would be for him to protect all of his sitting MPs from nomination battles, or determine criteria to shield MPs with healthy riding associations and expose others to challenges. What is certain is that another round of contentious nominations will be held in the ridings that are currently in the hands of the opposition.

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"The Liberal Party of Canada is committed to fair and open nominations, and we are proud of the five outstanding Team Trudeau candidates that local Liberals have nominated for ongoing by-elections across Canada," party spokesman Braeden Caley said.