Despite a court order halting most of his extreme vetting policy, President Trump’s administration has quietly been working toward his goal of a drastic cut in the number of refugees the U.S. will accept this fiscal year.

President Obama had set a target of up to 110,000 on his way out the door, but Mr. Trump tried to reset that number to 50,000. If the pace continues, the final tally is likely to be about 60,000 when the fiscal year ends in September — well below the level Mr. Obama wanted to lock in.

Most striking is the drop in the number of refugees from the seven terrorist-connected special interest countries that Mr. Trump singled out for extra scrutiny in his executive orders: Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen.

Those countries accounted for about half of all refugees admitted over the final months of Mr. Obama’s tenure. But during the past six weeks, they have represented only about a quarter of the refugees — despite a judge’s order instructing Mr. Trump to keep Mr. Obama’s policies in place.

Security analysts cheered the move, saying the new president has already changed the culture from the previous administration.

“Even if ‘extreme vetting’ is on hold, good vetting takes time, and the Trump administration’s plans to follow the law are eliminating the irresponsible rush to judgment that took place under the Obama administration,” said Matthew J. O’Brien, research director at the Federation for American Immigration Reform and a former senior anti-fraud executive at U.S. Citizenship and Immigration Services, one of the agencies that handles refugees.

Across two executive orders — one in January and, after courts blocked it, a revised one in March — Mr. Trump has tried to impose a 90-day halt on all admissions from a half-dozen suspect countries. He has also attempted to enforce a 120-day pause in refugee admissions and a broader halt to any Syrian refugees. He also cut Mr. Obama’s refugee ceiling by more than half, to just 50,000.

The goal, Mr. Trump said, was to give his administration a chance to improve screening procedures so no potential terrorists could slip through.

However a federal judge in Hawaii said Mr. Trump’s entire approach has been tainted by the “animus” he showed Muslims during the presidential campaign and has put all of the key parts on hold.

That means the Trump administration is still admitting refugees from the seven targeted countries of Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen — but at much lower levels than during Mr. Obama’s tenure.

Syrians made up about 15 percent of all refugees admitted during Mr. Obama’s time this fiscal year. Over the past six weeks, though, they total about 4 percent. The number of Iraqis has dropped from 15 percent under Mr. Obama to about 8 percent of the total in the Trump administration.

Overall, the number of refugees accepted worldwide has dropped from more than 10,000 in October to 2,070 in March, and only slightly more than 3,000 in each of the past two months.

The Justice Department late last week asked the Supreme Court to intervene in the court battle and allow Mr. Trump’s full travel ban and refugee halt to be reinstated — including a full stop to Syrian refugees and reimposing the 50,000 cap for fiscal year 2017.

If they succeed, it would slow refugees even more. The government has admitted more than 46,000 in the first eight months of the fiscal year, so that would leave an average of just 1,000 for each of the final four months — 10 percent the rate Mr. Obama had hoped.

Refugee advocates say thousands of refugees could be stranded without options.

“For people who may have family here who don’t know what the future means for them, that’s just a tragedy. For people who were in the process and now are wondering what’s next for them, and people who are in precarious and tenuous and vulnerable conditions, what does this mean for them? I don’t have an answer for every refugee, but in general it’s not a good situation for refugees,” said Kay Bellor, vice president for programs at the Lutheran Immigration and Refugee Services.

She said American communities have shown “an amazing outpouring of support” for the refugees and that the government needs to match that commitment. Ms. Bellor said a 50,000 cap is well below what the U.S. can — and should — accept.

“Disappointment is kind of not even a strong enough word,” she said. “The U.S. should do more. The problem is great, our resources are great.”

The U.S. looks to the U.N. High Commissioner for Refugees to conduct initial screenings to decide who would be good candidates for resettlement. American officials at U.S. Citizenship and Immigration Services then do their own screening, which includes an interview and the most extensive background check possible, and the State Department makes final approvals.

Refugees are resettled in the U.S. by nonprofit groups such as the Lutheran Immigration and Refugee Services.

Mr. Trump argues that the U.S. needs better refugee screening, and security analysts point to a number of people admitted as refugees who have been charged with terrorist-related offenses over the past decade. Refugee advocates counter that the rate of crime and other dangers from refugees is low.

For now, battles in Congress over budgets and in the courts over the legality of the president’s plans have left the agencies that administer the refugee program struggling.

USCIS began a slowdown in January to conform to Mr. Trump’s 50,000 ceiling. When a judge in Hawaii issued an injunction in March halting the 50,000 number, USCIS had to alter its plans but had already canceled interviews with thousands of potential refugees.

Now, the agency is scrambling to adjust the pace of interviews.

The State Department blamed an uncertain budget situation for the overall slowdown and suggested that activity would pick up after Congress approved funding for fiscal year 2017 in early May.

The department said in a statement that it is acting under the 110,000 ceiling set by Mr. Obama but stressed that is an outer limit, not a target.

“We are not in a position to speculate as to the final number of refugees that will be admitted by the end of this fiscal year,” the department said.

The department declined to answer why the percentage of refugees from special-interest countries has dropped, saying only that “we continue to interview and process refugees of all nationalities.”

Mr. O’Brien said part of the slowdown from special-interest countries could be a result of deteriorating conditions in the Middle East in recent months.

But overall, he said, the numbers are a signal that Mr. Trump is in charge and employees are getting the message.

“Many of the people from the Iraq/Syria region under the Obama administration should never have been admitted to the United States. It appears that the Trump administration is making attempts to engage in serious (as opposed to superficial) vetting efforts and is approving refugee applications only for individuals who appear to be genuine refugees,” Mr. O’Brien said in an email.

He also said he suspects that where the Obama administration treated the refugee cap as a target to be met, the Trump administration sees it as an outer limit.

“Part of Obama’s immigration agenda was to significantly increase the number of both asylees and refugees admitted to the U.S. — presumably because President Obama saw the U.S. as being responsible for the degradation of the security situation in the Middle East. By way of contrast, President Trump has clearly indicated that he sees refugee admissions as a priority national security issue and radical Islam as the source of the problem,” Mr. O’Brien said.

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