The president has argued that the recent caravans are a threat to national security. Another judge rejected the administration's request to try to detain migrant families in long-term facilities.
The judge's ruling will remain in effect for one month, with another hearing scheduled in December to consider arguments for a permanent order.
The final version of the order was upheld by the US Supreme Court on June 26 after a protracted legal battle.
It said, "As the Supreme Court affirmed this summer, Congress has given the President broad authority to limit or even stop the entry of aliens into this country".
"We will take all necessary action to defend the executive branch's lawful response to the crisis at our southern border", the statement concluded.
That way, the official said, courts will "handle those claims in an expeditious and efficient manner, so that those who do actually require an asylum protection get those protections". The law states that migrants crossing the border at any point can ask for asylum.
"Sec. Nielsen's false comments about the Refugee Exodus are a deliberate attempt to mislead the public and demonize refugees fleeing government sponsored violence and displacement", the group said. He said he did not travel with any of the caravans. Legal groups sued hours after the proclamation was issued, arguing USA law clearly allows someone to seek asylum regardless of how they enter the country.
He was spurred on by the approach of several migrant caravans, with thousands of people who he said included "criminals" and "very bad thugs and gang members". "There is no justifiable reason to flatly deny people the right to apply for asylum, and we can not send them back to danger based on the manner of their entry". But - illegal crossings overall are well below historical highs from previous decades. The Justice Department has not said yet whether they will appeal the ruling, which is in effect for a month.
The president's proclamation on November 9 attempted to limit asylum to immigrants who crossed at designated ports of entry and deny asylum to those who entered at other locations along the 2,000-mile southern border.
The president issued a proclamation on 9 November declaring that anyone who crossed the southern border between official ports of entry would be ineligible for asylum. Officials didn't say whether those people's cases were still progressing through other avenues left to them after the proclamation.
A lawyer for the Center for Constitutional Rights said the law "couldn't be clearer". But many border crossings, such as in San Ysidro, have long waiting times. People are often forced to wait in shelters or outdoor camps on the Mexican side, sometimes for weeks.
US border inspectors are processing only about 100 asylum claims a day at Tijuana's main crossing to San Diego. "Today, we are using the authority granted to us by Congress to bar aliens who violate a Presidential suspension of entry or other restriction from asylum eligibility".
"There is a legal and illegal way to enter the U.S. We have deployed additional forces to protect our border".