Maldives President Mohamed Waheed wrote to Prime Minister Stephen Harper to complain about Baird's conduct during recent Commonwealth meetings in New York.
In a statement posted on the Maldives president's website, Waheed alleges Baird made "inappropriate and derogatory remarks" and "posed several harshly worded questions" to his acting foreign minister.
The remarks pertained to "domestic politics in the Maldives," according to the statement, but Baird's exact words remain unclear.
Baird's office says the minister raised concerns about the first round of voting in the Maldives' presidential election, which the country's highest court on Monday declared was flawed, as well as reports of violence and intimidation.
Still, Baird's conduct has "put unnecessary pressure on an otherwise excellent relationship" between Canada and the small island nation in the Indian Ocean, the Maldives statement said.
Waheed alleges the comments were made during a meeting of Commonwealth foreign ministers on the sidelines of last month's United Nations general assembly.
An official with the Maldives embassy in New York, who spoke on condition of anonymity because he was not authorized to speak publicly, said Baird's comments contained a "personal bias."
"The president was concerned by an expression and an admission of personal bias by the honourable minister, detriment to our bilateral relationship and contrary to the high esteem to which we hold the Canadian government and people."
Baird's office was not shying away from the controversy Monday. Spokesman Rick Roth said the minister was voicing concerns about the delay of the Maldives' run-off election and reports of violence and intimidation.
"He also pointed out the irony of the acting foreign minister of the Maldives representing that country at (the Commonwealth Ministerial Action Group), when her president received five per cent of the vote in the first round of the election," Roth said in an email.
"Perhaps that is where President Waheed took offence."
Roth also said Baird "pointed out to (action group) members that the second round of elections have been 'suspended' under mysterious circumstances and called on Maldivian officials to proceed with the second round of elections without delay."
The Supreme Court of the Maldives on Monday annulled the results of the first round of voting in the country's presidential election, saying thousands of votes cast last month were tainted.
Roth also noted it is not the first time Baird has raised concerns about the Maldives.
"The minister believes that countries within the Commonwealth should adhere to a certain standard of values and principles, which is clearly lacking in the Maldives," he wrote.
Harper, who is in Southeast Asia this week for the Asia-Pacific Economic Co-operation meeting, on Monday adopted a similar tone toward Sri Lanka over its ongoing human rights abuses.
The prime minister said he plans to boycott next month's Commonwealth summit in Sri Lanka, and he threatened to cut the roughly $20 million Canada gives each year to various Commonwealth initiatives.
— With files from The Associated Press
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