A court order sentencing a draft registration resister to work at a Veterans Administration hospital in Virginia has been withdrawn by a federal judge after the VA objected to the sentence.

Enten Eller, 21, the first person convicted of refusing to register under a standby draft system set up in 1980, was ordered earlier this month to begin two years' unpaid service in July at a VA hospital in the Roanoke area. U.S. District Judge James C. Turk rescinded his week-old order, however, after being told that U.S. officials might go to court to attempt to block it.

"The purpose of the VA is inconsistent with having this fellow put into our hospital," VA general counsel John P. Murphy said yesterday. "Our hospital is to take care of those who served."

Mike Duncan, a federal probation supervisor in Roanoke, said he urged Turk to withdraw his order after learning that VA and Justice Department officials might challenge it. If the VA hospital, in neighboring Salem, became the focus of court conflict, Duncan said, "the place would no longer be amenable. Too much controversy would be created."

Eller, a member of the pacifist Church of the Brethren and an honors student at the church-affiliated Bridgewater College in the Shenandoah Valley area, has said God directed him not to sign up for the draft. Turk has found Eller's beliefs to be sincere.

Jonathan M. Rogers, one of Eller's lawyers, said he spoke with Eller on Thursday about the withdrawal of Turk's earlier order. "He's certainly a little surprised but he's not disappointed," Rogers said. He added that Eller had feared he might receive a "hostile" reception from VA hospital employes who "resented him or what he believed in."

Rogers and Duncan said they will urge Turk to sentence Eller to perform alternative service at another hospital, social service organization or similar agency not connected with the VA. Eller was not available for comment yesterday.

During World War II, conscientious objectors were permitted to serve in military hospitals and as Army medics. These individuals were not, however, convicted of any offense. A VA spokesman said yesterday that no precedent has been established in recent years for assigning opponents of the draft or war to VA hospitals.

In his brief order, issued Wednesday, Turk gave no explanation for rescinding his earlier decision. After Eller's Aug. 17 conviction, Turk rejected requests by prosecutors that Eller receive a two-year prison term. Initially, Eller was placed on three years' probation and ordered to register for the draft within 90 days. When Eller failed to register, Turk sentenced him to alternative service.

Duncan said he believed the VA had come under "strong pressure" from national veterans groups opposed to having Eller work at a VA hospital. But VA counsel Murphy denied this contention, saying the VA had taken the initiative. "The idea that they pressured us--they certainly did not pressure me," Murphy said.

Murphy said, nevertheless, that he had discussed the issue with American Legion officials. "We were concerned that this type of thing should not be used as punishment," said American Legion spokesman Jim Witek.

Murphy said the VA had asked Justice to weigh the possibility of filing a court motion asking Turk to reconsider his March 2 order for two reasons. One was that it was inconsistent to assign a man convicted of violating registration laws to a hospital serving men drafted in past wars, and the other was that the VA was troubled at being the subject of a court order without having participated in the legal proceedings.