The adverts made it appear respondents were taking part in the official 2020 US census, which begins on 12 March.
They were promoted by a fundraising group backed by Republican officials and Mr Trump’s re-election team.
“There are policies in place to prevent confusion around the official US census,” Facebook said.
“This is an example of those being enforced,” said the spokesperson.
The adverts began running on Facebook on 3 March. Clicking the link takes users to a general survey focusing on Republican talking points.
The adverts were paid for by the “Trump Make America Great Again Committee”, a part of Mr Trump’s official re-election fundraising efforts.
It is backed by the Trump campaign and the Republican national party.
It owns and operates the Facebook pages of both Donald Trump and Mike Pence, which ran the controversial adverts.
The adverts were “deceptive” and “unacceptable”, said Vanita Gupta, president and CEO of The Leadership Conference on Civil and Human Rights, which helped Facebook craft its policy on census interference.
“If Trump says a fake census is ‘official’, people are going to think its official,” she said in a series of tweets. “Trump’s deceptive ads will confuse people about how and when to participate in the 2020 Census, threatening their right to get counted and bring resources and political power to their communities.”
Facebook has come under pressure to increase its role in blocking political interference in the past.
Those who clicked the link in the advert were sent to a page on the Donald Trump website where they were asked to complete a survey.
The survey begins by asking about age and political leaning, before asking questions about Trump talking points such as “Obamacare”, “the Democrats’ failed Impeachment Witch Hunt” and “Nancy Pelosi and the Radical Left”.
Those who fill out the Trump campaign’s “census” are ultimately sent to a web page calling for donations.
The BBC saw more than three hundred versions of the advert, each targeting different states and demographics.
For example, one advert specifically targeted men aged over 45 in Texas, whereas another targeted women aged over 45 across the US.
Most adverts were aimed at older people, with one exclusively targeting men and women aged over 65 in Maine, Florida, Arkansas and Arizona.
It is not clear exactly how many adverts were run, or how many people would have seen them, only that most of the adverts had been seen by fewer than one thousand people.
The official census is mandated under the US Constitution and takes place every 10 years, counting every resident.
The census has political implications as it is used to determine the number of seats each state holds in the House of Representatives, as well as how federal funding is allocated for the next 10 years.
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