BALTIMORE, AUG. 21 -- A Maryland animal trapper was ordered today to serve 16 days in jail for fatally shooting a bald eagle, the first such sentence here in recent years for killing the endangered bird and national symbol.

Carlton R. Thomas Jr., 36, of rural Dorchester County on Maryland's Eastern Shore, acknowledged shooting the eagle but contended that he was only trying to scare it away from a muskrat trap.

"It was an accident . . . . I'm very sorry," the heavy-set, bearded outdoorsman told U.S. Magistrate Daniel E. Klein Jr.

The eagle, shot through both legs, was found wounded in the marshy backwaters of Dorchester County on Feb. 17 but died June 1 after federal authorities spent more than $4,000 trying to keep it alive.

Under terms of a plea agreement, Thomas was ordered by Klein to serve eight consecutive weekends in jail, beginning after the Chesapeake Bay crabbing season ends Nov. 1.

Prosecutors agreed to the arrangement and to forgo a fine because of Thomas's low income. The hunter's attorney, Larry A. Ceppos, said Thomas earned $7,500 in 1989 and has $21.29 in a checking account and $500 in a savings account. Thomas faced a possible maximum sentence of one year in prison and $100,000 in fines.

In a case that at times resembled a murder mystery, FBI ballistics experts traced the bullet found in the eagle's leg to a rifle used by Thomas.

The expense of the law enforcement effort was worth it, said Breckinridge L. Willcox, Maryland's chief federal prosecutor, because "We take these offenses very seriously . . . whether or not there was an intent to kill the bird."

Known for his strong stand against environmental crimes, Willcox said, "Anyone shooting bald eagles in this state should assume they will have the oportunity to contemplate their actions from the comfort of a jail cell."

Thomas, a lifelong hunter and waterman whose father is a retired Maryland Natural Resources Police officer, makes his living crabbing, trapping muskrats for food and pelts and bounty-hunting for nutrias, large rodent-like predators for which the state pays $1 a pelt.

According to Assistant U.S. Attorney Christopher B. Mead at today's hearing, two fishermen reported finding the wounded eagle near the Blackwater National Wildlife Refuge. Rangers rushed the bird to an animal rescue facility, but despite six hours of surgery and the removal of a bullet from its right leg, it eventually died.

Meanwhile, the FBI was brought in. Examining the markings on the slug taken from the eagle's leg, Mead said, agents were able to identify it as a .22 caliber Winchester magnum copper bullet fired by one of five models of the .22 Marlin rifle.

The FBI passed the information on to U.S. Fish and Wildlife Agent Frank T. Kuncir, who monitors outdoorsmen in Dorchester County. Kuncir saw Thomas with a Marlin rifle and confronted him.

Thomas admitted shooting at a "large bird" on Feb. 9 but said he did not know it was an eagle. It flew away, he said, and he did not realize it had been hit.

After Thomas surrendered his rifle, agents confirmed that it had fired the fatal shot. He was charged with shooting a bald eagle "in wanton disregard for the consequences."

Glenn Therres, a Maryland Forest, Park and Wildlife supervisor, said there had been no similar prosecutions in Maryland since 1985 and few, if any, before that. He said the state's 123 breeding pairs of bald eagles have produced 164 young this year. There were about 2,660 nesting pairs in the United States, excluding Alaska and Hawaii, in 1989.