A federal judge on Tuesday put on hold the deportation of several dozen Indonesians in New England who had lost their bid to remain in the U.S. and feared persecution if returned home.

The nearly 60 Indonesians in New Hampshire and Massachusetts are mostly Christians and fled religious persecution before and after the fall of the country’s former dictator, Suharto, in 1998. In the chaos that followed, riots broke out and mobs targeted ethnic Chinese and other minorities in the mostly Muslim country.

A lawsuit on their behalf was filed Monday. A judge in Boston ruled Tuesday that U.S. immigration officials could not remove the Indonesians until a determination was made about whether the court has jurisdiction.

“I’m tremendously relieved that the court has issued this injunction that delays deportation for members of New Hampshire’s Indonesian community,” Democratic U.S. Sen. Jeanne Shaheen of New Hampshire said in a statement. “The court’s action today provides valuable time to continue making the case for why the Indonesian community should remain in New Hampshire.”

Many of the Indonesians came to seacoast communities in New Hampshire, where they found jobs and raised families. In a deal brokered by Shaheen in 2009, they were allowed to stay as long as they regularly reported to the Immigration and Customs Enforcement office.

But in recent months, they have been told during their visits to the immigration office that they should buy plane tickets and prepare to leave the country. Some said they fear returning due to an uptick in intolerance and violence against Christians and other minorities.

“Sadly, they are being caught in this immigration net that was designed to address people here illegally who may have a criminal background. These folks aren’t in that situation,” Shaheen said. “They came here seeking asylum from religious persecution so I think we need to look at how we can make sure our system is not one size fits all — that it addresses the individual needs of families.”

Sarah Jane Knoy, who heads a non-partisan community organization, said the move to deport the Indonesians “runs counter to what I believe are American values.”

“I think that it’s unconscionable that ICE is trying to deport people who came here fleeing persecution and physical violence,” said Knoy, executive director of the Granite State Organizing Project.

She speculated they are being targeted “because they are low-hanging fruit. They have been checking in regular, are law abiding and are easy to find.”

Shawn Neudauer, a spokesman for ICE, said a judge already had ruled the Indonesians had to leave the country and that they had been given to up to two years “to pursue forms of immigration relief” or get their affairs in order.

“The removal of aliens with lawfully issued Final Orders of Removal is done consistently throughout New England,” Neudauer said in a statement. “This is done without regard to their country of origin. ICE does not discriminate against any group of people.”