Nikki Haley didn’t wait to take office as U.S. ambassador to the United Nations to break with the Trump administration’s foreign policy stances.

At her Senate confirmation hearing, Ms. Haley bluntly accused Russia of being complicit of war crimes in Syria going against the president-elect’s talk of warmer relations with Moscow.

Three months later, she remains boldly off-message. Much to the chagrin of Washington diplomats, her remarks often go well beyond the carefully worded scripts crafted by the White House and State Department.

She’s warned Syrian President Bashar Assad that “the days of your arrogance and disregard of humanity are over,” even as other top aides to President Donald Trump insisted that his fate was a decision for the Syrian people.

She’s pushed human rights as a driver of foreign policy just as the Trump administration showed its willingness to work with leaders who have suppressed civil liberties, such as Turkey’s Recep Tayyip Erdogan and Egypt’s Abdel-Fatah el-Sissi.

U.S. diplomats fear Ms. Haley’s words could result in an inconsistent, incoherent international message. State Department diplomats drafted an email urging Haley’s office to ensure that her public statements on high-profile issues are cleared by Washington. The email was first reported by The New York Times.

In some ways, Ms. Haley has been ahead of the curve. Her hints at a change in the Syrian government are now seeping into Trump policies, and the administration has toughened its stance on Russia.

She seems to be in Mr. Trump’s good graces. At a White House luncheon for U.N. diplomats last week, he said Ms. Haley was doing a “fantastic job” but only after awkwardly joking that if the diplomats didn’t like her, “she could easily be replaced.”

As South Carolina governor, she was outspoken in her criticism of Mr. Trump during the 2016 campaign a stance that effectively disqualified other candidates for top administration positions. The daughter of Indian immigrants, Ms. Haley alluded to Mr. Trump in denouncing “the siren call of the angriest voices” who disrespected America’s immigrants. Mr. Trump tweeted that “The people of South Carolina are embarrassed by Nikki Haley.”

She has star power in an administration where the President prefers to keep attention on himself. In some ways, the 45-year-old Ms. Haley is seizing the spotlight left vacant by media-averse Secretary of State Rex Tillerson. Her high-profile persona and relative youth have prompted speculation that she may run for president someday.

The White House and the U.S. Mission to the United Nations declined to comment for this story.

The officials spoke on condition of anonymity because they weren’t authorised to publicly discuss the policymaking process.

They said the State Department was not involved in the planning of Mr. Trump’s meeting last Monday with the U.N. ambassadors, nor was it consulted. The event was coordinated exclusively between the U.S. Mission to the U.N. and the NSC.

Public remarks by the U.N. ambassador are generally approved by the State Department and, at times, other departments. Zalmay Khalilzad, a U.N. ambassador under President George W. Bush, said that messaging from the various departments has “to be consistent with each other,” but he joked that this is not an administration that is “known for protocol.”

Indeed, Ms. Haley’s off-message remarks highlight a broader trend in the administration, with poor communications and tight inner-circle White House politics creating disunity on various issues.

But Mr. Khalilzad praised Ms. Haley, saying her “experience as a politician helps her in recognizing the importance of the message and the quality of the message.”

Phil Cox, a political consultant who has known Ms. Haley since 2010 from his work with the Republican Governors Association, said Ms. Haley’s plain-spokenness comes as no surprise to anyone who tracked her work in South Carolina, starting with service in the state Legislature.

“The Nikki Haley operating on a world stage today is the exact same person the people of South Carolina came to know and respect as governor,” he said in a recent interview. “Since she was first elected governor, people have been talking about her taking the next step.”