Ken Isaacs, the U.S. nominee to lead the U.N. migration agency, was knocked out of the race on Friday after coming third behind Portugal's Antonio Vitorino and Costa Rica's Laura Thompson in a secret ballot of member states in Geneva, delegates said.
After four rounds of voting, Vitorino, a former European Commissioner and Portuguese deputy prime minister, was declared the winner by acclamation, and will lead the International Organization for Migration for a five-year term.
Isaacs, vice president of U.S. evangelical charity Samaritan's Purse, had caused controversy after being forced to apologise for tweets and social media posts in which he disparaged Muslims.
The leadership race comes at a crucial time for global migration politics, as U.S. President Donald Trump attracts criticism for his "zero tolerance" policy on the Mexican border and the European Union struggles to find unity on how to deal with the influx of mainly African migrants across the Mediterranean.
The job has traditionally gone to an American, but before the election some diplomats predicted that the changing status of IOM, which joined the U.N. family in 2016, and the wide-open election might cause governments to challenge that assumption.
The White House had strongly backed Isaacs, despite U.S. withdrawal from other international bodies and agreements, such as the U.N. Human Rights Council.
"The choice of who will be the new director of the International Organization for Migration will be extremely important for U.N. action in respect of migration," Elspeth Guild, a migration expert and law professor at Queen Mary University of London, told Reuters earlier this week.
"And I think that it will also be terribly important in seeking to resolve and perhaps take some of the sting out of some the migration politics that are perturbing international relations at the moment."
Keith Harper, who served as U.S. human rights ambassador under President Barack Obama, said in a tweet that Isaacs' rejection was "yet another sign that U.S. power, authority and prestige has been so dramatically diminished".
The election continued after Isaacs dropped out, with the winner needing two-thirds of the votes.
Delegates said the first three rounds were led by Vitorino. Thompson, currently deputy head of IOM, came second, while Isaacs' share of the vote shrank in each successive round.
During the 1990s, Vitorino was a minister in the Portuguese government of Antonio Guterres, now U.N. Secretary General.