Under the State Department's new requirements, the USA will only recognise marriages, rather than same-sex partnerships, when granting diplomatic visas to partners.
But the official denied the move was "punitive" or an "attack", saying it was needed to ensure compliance with the Supreme Court decision to legalise same sex marriage in 2015. "The ones really impacted are those who will have difficulties going to a country that performs same-sex marriages".
David Pressman, who served as United States ambassador to the UN Security Council for special political affairs under President Barack Obama, said the policy change was so damaging because the UN was "composed of probably one of the most diverse workforces of any organization in the world".
While the couples have until January 1 to get married - and could do so in the United States - they could be arrested and prosecuted when they return home if homosexuality is illegal there.
Currently, 25 countries have recognised same-sex marriage.
The United Nations sent a memo to staffers in September regarding the impending change.
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The State Department under Mr Trump has not filled a position created by former secretary of state John Kerry of a special envoy advocating LGBTQ rights around the world.
In a statement published on its website on October 1, the State Department has warned: "Effective immediately, U.S. embassies and consulates will adjudicate visa applications that are based on a same-sex marriage in the same way that we adjudicate applications for opposite gender spouses".
The State Department gave affected couples until December 31 to marry, either in the United States or in a third country where same-sex marriage is illegal, and present a valid marriage certificate.
"US diplomats as of yesterday have to be legally married in order to get this sort of derivative diplomatic status when they go overseas, so these changes are to mirror what USA policy now is", one of the senior administration officials said, speaking on condition of anonymity.
An exception in the policy applies for same-sex partners of diplomats coming from countries that do not recognize same-sex marriage, but do accredit same sex spouses of American diplomats.
"Those not yet in the country will need to show they're married to secure a visa, potentially forcing those living in countries without marriage equality to choose between a posting at UN headquarters or family separation", Akshaya Kumar, deputy United Nations director at Human Rights Watch, wrote in a blog post.
The senior Trump administration official said the United States will have a process to recognize same-sex domestic partners of foreign diplomats from countries where same-sex marriage is not legal, but which recognize American domestic partners. Twenty-six countries allow gay marriage, according to a 2017 tally by the Pew Research Center.