Dr Pankaj Satija and his wife Dr Monika Ummat, both neurologists, have been working legally in the US for the last 15 years.
As they were about to board a plane for India yesterday, they were granted a 90-day extension on humanitarian grounds.
The problem started when they visited India to see Pankaj's sick father in October last year. On their return they were stopped at the Bush International airport by Customs and Border Protection officials because their travel documents had expired, the Houston Chronicle reported.
Upon returning to the US about a week later, a Customs and Border Protection official at the airport noted the discrepancy. The officials, however, allowed them to enter temporarily to correct the error.
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On Wednesday, Pankaj and his wife were abruptly told by immigration officials that they had 24 hours to leave the US. The couple, who have a 7-year-old son and 4-year-old daughter, were told that under a new policy, they could no longer extend their temporary permission to stay while they waited for permanent authorisation, local media reported.
They reported, as ordered, to customs officials at Bush Intercontinental Airport, where they were told the agency had suddenly reversed course.
"Somebody at a higher level has made that decision," they were told by an agent. "I understand that you are physicians and a lot of lives are at stake."
The agency offered the couple three months of humanitarian parole, a rare measure allowing immigrants, who are otherwise not permitted to enter the US, the opportunity to do so due to a "compelling emergency" to sort out their paperwork.
The US administration last month issued tough new orders to begin a sweeping crackdown on undocumented immigrants, putting nearly all of the country's 11 million undocumented foreigners in target for deportation.