The president’s eldest son made the analogy in a social media post, amid a lengthy government shutdown caused by a dispute over funding for the proposed barrier on the US border with Mexico.
“You know why you can enjoy a day at the zoo? Because walls work,” Mr Trump Jr wrote on Instagram.
His comments were immediately denounced by other social media users.
Seinfeld director Larry Charles tweeted that Trump's oldest son was “so blinded by his own hubris that he can't see that once @realDonaldTrump falls, he will be nothing but a convict serving time for treason, in a cage, behind a wall.”
Emily Jane Fox added: “Immigrants as caged animals, from the First Son.”
The comments were also described as “ill-considered at best” and “racially insensitive”, by CNN commentator, Van Jones. “If you have the slightest bit of sensitivity on these types of issues the one thing you don’t do is compare low income, Latino, brown people to zoo animals,” he said.
Mr Trump Jr’s post followed a televised Oval Office address from his father on Tuesday evening, in which he said the nation was facing a “humanitarian crisis” on its southern border.
The president used the speech to call on Democrats to negotiate a funding deal, the lack of which has seen parts of the government shut down for more than 19 days and left 800,000 federal employees either furloughed or working without pay.
However, Mr Trump is said to have walked out 30 minutes into a White House meeting with top Democrats on Wednesday, after they refused to allocate $5.7bn (£4.5bn) for his border wall.
Senate minority leader Chuck Schumer claimed the president’s behaviour at the meeting amounted to a “temper tantrum”, during which he “slammed the table” before storming out of the room.
Mr Trump later tweeted the discussions had been a “total waste of time”.
“I asked what is going to happen in 30 days if I quickly open things up, are you going to approve Border Security which includes a Wall or Steel Barrier?” he wrote.
“[House speaker] Nancy [Pelosi] said, NO. I said bye-bye, nothing else works!”
He denied the president had lost his temper during the meeting, telling reporters outside the White House: “I don’t recall him ever raising his voice”.
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