Almost 400 of the animals were being held in corrals inside the park for testing to see if they have been exposed to the disease brucellosis.
Officials had planned to begin this week sending to slaughter those bison that test positive.
But environmental and American Indian groups are seeking a restraining order from a federal judge in Helena to block the shipments. No shipments are expected while the legal challenge is reviewed by the Park Service, Yellowstone spokesman Al Nash said.
Brucellosis can cause wildlife and livestock to prematurely abort their young. About half the park's bison carry the disease, although no bison-to-cattle transmissions have been recorded.
"Our plan at the moment is to continue testing and sorting these animals. We'll see what next week brings," Nash said.
Court filings indicate the government plans to respond to the request for a restraining order by Monday. No hearings have been set. The case is before U.S. District Judge Charles Lovell.
The legal maneuvering comes as the park's iconic bison herds are suffering their worst winter in several years, with deep snows forcing many of the animals out of the park and a much-heralded initiative to expand where they can roam is on the verge of failure.
Park workers and state livestock agents have been trying for the last several weeks to halt the animals' exodus from the snow-packed park to lower elevations.
Bison periodically attempt to migrate out of the park in search of food. But many end up in government-operated corrals under a controversial program meant to guard against the spread of the disease brucellosis to livestock.
Christian Mackay, executive officer of the Montana Department of Livestock, said Friday that scheduling shipments of any captured bison is primarily a federal responsibility.
Through Friday, 224 of the 368 captured bison had been tested. Seventy-six tests came back positive and 148 negative, park spokesman Al Nash said.
There is no guarantee the negative animals will be released. Holding them until spring in the corrals along the park border could prove impossible if bison keep pouring out of the park.
The corrals hold only about 400 animals.
Those involved in the legal challenge said the chance of livestock being infected by bison is too low to justify the death of so many bison - the largest wild land animals in North America.
"It doesn't make sense why they have such a lethal approach," said Tom Woodbury with the Western Watersheds Project, one of the plaintiffs in the case. "There are no cattle on public lands (adjacent to the park) this time of year. This seems to be more about population control than disease control."
Meanwhile, a $3.3 million initiative to give a small number of bison more to roam outside the park was down to a single animal.
It has been just two weeks since 25 of the burly animals were herded onto the Gallatin National Forest, where bison had been prohibited for decades. But some of them repeatedly left the 2,500-acre patch where they were supposed to spend the winter. One was shot after entering private property, and 23 were captured and shipped back to the park or returned there on their own.
Government officials said it was uncertain when or how they would attempt again to carve out new habitat for the species in Montana. The state's Democratic governor, Gov. Brian Schweitzer, suggested another batch of 25 bison could be herded from the park down to the forest land, but there were no immediate plans to do so.
Few cattle remain in the immediate vicinity of the park. Wildlife advocates said those conditions make it possible for government agencies to ease their restrictions on where bison can move.
But a spokesman for the Montana Stockgrowers Association said the livestock group is closely tracking the pending legal case and remains wary of any move to expand where bison can roam outside Yellowstone.
Jay Bodner, the association's director of natural resources, said cattle producers whose animals are infected with brucellosis can face economic losses if buyers are not willing to pay as much for their animals.
"Management actions still need to be taken," he said in reference to the government-sponsored capture and slaughter program.
In 2008, a record 1,600 bison were killed leaving the park, including more than 1,400 that were shipped to slaughter.