"Such absolutely discriminatory measures that only happen over people's race, nationality or religion are against international human rights laws and principles," foreign ministry spokesperson Abbas Mousavi said.
"These individuals were questioned by America's border security over their political views and beliefs, and their social media accounts were forcefully entered," he said in a statement.
US says 34 troops diagnosed with traumatic brain injury after Iran strike
US media reported on Monday that an Iranian student headed to a Boston university had his visa cancelled at the airport and was deported by immigration officials.
Tensions have soared between Tehran and Washington since a US drone strike killed top Iranian general Qasem Soleimani in Baghdad on January 3.
Iran retaliated five days later by launching a wave of missiles at US troops stationed in Iraq.
Tehran was still on high alert hours later when its air defences mistakenly shot down a Ukraine International Airlines passenger jet, killing all 176 people on board.
Soleimani's successor to face same fate if he kills Americans, warns US diplomat
"These actions against Iranians are in line with the American regime's hostile and hateful policy against Iran... now manifested in harassing Iranians at America's borders," Mousavi said.
The spokesperson warned the United States could face action "through human rights bodies", without elaborating.
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