Mohammad Shahab Dehghani Hossein
CNN  — 

An Iranian student planning to attend Northeastern University was flown out of the United States despite an emergency stay, and Customs and Border Protection said it was not aware a court had temporarily blocked the student’s removal.

Mohammad Shahab Dehghani Hossein, 24, was refused entry to the United States on his student visa when he arrived at the Boston Logan International Airport on Sunday. While he was detained, a Massachusetts district court judge granted him an emergency stay but he was deported Monday night, said his attorney, Kerry Doyle.

Customs and Border Protection was “unaware of the issuance of any court order barring the removal of the subject from the United States” when Dehghani boarded the flight and the aircraft’s doors had closed, the agency said in a statement.

Judge Allison D. Burroughs ordered Monday that Dehghani’s removal be stayed for 48 hours or until further order of the court, according to the court docket. A federal detention hearing for Dehghani was scheduled for Tuesday morning.

Tuesday, Judge Richard Stearns said the case is now “moot” because Dehghani was “never admitted into the United States, is no longer in custody, and the court does not have jurisdiction to order his return,” CBP said in a statement.

Northeastern University said it has not received a “satisfactory explanation” from Customs and Border Protection for the student’s deportation.

“We believe that a clear explanation is needed, especially because the deportation took place after a 48-hour extension was granted by a federal judge. Only in the most extreme instances should students have their academic pursuits interrupted by government intervention,” the university said in a statement.

Immigration and Customs Enforcement said it is not involved in the case.

The student’s visa was revoked, his attorney says

According to an emergency petition filed by Doyle, the State Department issued Dehghani a student visa last week. But when Dehghani tried entering the United States on January 19, he was taken into secondary inspection and refused entry.

US Customs and Border Protection revoked Dehghani’s student visa and issued him an expedited removal order, the court filing says.

“It is unclear why Defendants would now decide, after conducting a full visa issuance process, that Plaintiff’s student visa should be revoked,” the court document say.

The defendants in the filing include CBP and the Department of Homeland Security.

“Rather than being based in legitimate concerns over Plaintiff’s admissibility to the United States, this revocation and expedited removal is a result of additional scrutiny targeting Iranian citizens,” the filing says.

In a statement, CBP said it could not discuss individual proceedings.

“CBP officers are charged with enforcing not only immigration and customs laws, but they also enforce over 400 laws for 40 other agencies and have stopped thousands of violators of US law,” the agency said in a statement.

“Applicants must demonstrate they are admissible into the US by overcoming all grounds of inadmissibility including health-related grounds, criminality, security reasons, public charge, labor certification, illegal entrants and immigration violations, documentation requirements, and miscellaneous grounds.”

Northeastern University also said it has been in touch with federal officials to learn more about the case and provide Dehghani with the appropriate assistance to “facilitate a successful return to Northeastern.”

Dehghani was admitted to the university’s undergraduate program starting in the 2018-2019 academic year and filed for a student visa in 2018. After an in-person interview and a full State Department review, he was issued his student visa last week, his court petition says.

Protesters rallied outside the airport

Meanwhile, a crowd of people including members of the ACLU of Massachusetts and the Muslim Justice League gathered at the Boston airport to protest Dehghani’s detention.

“In America, nobody is above the law – including Customs and Border Protection officials. Given the Trump administration’s xenophobic policies and CBP’s troubling practice at Logan Airport of sending students with valid visas back to Iran, it is shameful that the government defied a federal court order and deported Shahab without due process,” ACLU of Massachusetts Executive Director Carol Rose said in a statement.

“We are looking at all options to hold CBP accountable for wrongfully deporting Iranians and other students who hold valid visas.”

The ACLU of Massachusetts says at least 10 students have been sent back to Iran upon arriving to US airports, with seven of them having flown into the Boston airport.

Democratic presidential candidate and Sen. Elizabeth Warren of Massachusetts also weighed in, tweeting Monday: “Shahab Dehghani is an Iranian student with a valid F1 visa, returning to finish his education. CBP already held him overnight. His deportation must be halted, and we must fight the Trump administration’s xenophobic policies.”

CNN’s Geneva Sands, Nicole Chavez and Holly Yan contributed to this report.