An Army court-martial has acquitted a sergeant on charges of larceny and dereliction of duty in the first of four trials stemming from an investigaton into the Army's intelligence and special-operations units.

Master Sgt. Ramon Barron was acquitted late Saturday night at the end of a week-long court-martial held under tight security at the Army's Arlington Hall. Earlier in the trial, Col. James E. Noble, the military judge, found Barron not guilty on charges of filing false travel vouchers stemming from his classified missions.

Barron had been accused of stealing government funds while on covert missions for the Army by not completely accounting for cash advances. His court-martial is part of a larger investigation that is attempting to account for more than $150 million spent on the missions between 1981 and 1983.

Three other soldiers are facing charges. Army investigators have questioned scores of Army intelligence officials and ordered collections of at least $50,000 in allegedly misspent funds, according to informed sources.

A central issue in the court-martial is whether conventional Army spending regulations covered the money that, according to testimony at the trial, had been deliberately "laundered" by the Army to prevent it from being traced to the service when used in covert missions.

Barron's acquittal, after 70 minutes of deliberation by a panel of seven soldiers, is likely to fuel the controversy over the investigation that is almost two years old. Military and civilian critics say the military is unfairly trying to apply conventional regulations to covert, classified missions.

"It was recognized that the traditional ways of handling money were inappropriate to some of our missions," said an Army source familiar with the investigation and with some of the covert operations. "It's not fair to say our organizations were irresponsible in how they handled money or regulated it. It was a new program, and the investigators caught it at an immature point."

Army Vice Chief of Staff Gen. Max R. Thurman has declined to discuss the investigation.

"I feel great," Barron said yesterday. "After all the suffering for two years, finally the truth came out that there was no wrongdoing. All the agony me and my family have gone through will never be corrected, but it goes to show there is justice."

Barron, 42, who has been in the Army 25 years, was suspended from his duties in counterintelligence in December 1983, and his superiors refused to tell him the allegations against him. He was charged in May of this year.

He was the lowest-ranking of the four men charged. His former boss, Lt. Col. Dale C. Duncan, and two other officers who worked on classified missions, Lt. Col. Frederick Byard and Col. James Longhofer, are facing charges.

Duncan, who ran an Annandale-based front company called Business Security International that provided security for Army classified missions, was indicted last week on charges of defrauding the government.

Much of the testimony last week at Barron's court-martial was closed to spectators without security clearances. When the court was in session, the makeshift courtroom in an office of Building A at Arlington Hall was secured with a coded, electronic lock.

Open testimony centered on details of travel vouchers and expense reports Barron submitted to his superiors to account for travel advances while working at Business Security International. Military prosecutor Capt. Christoper Maher questioned government witnesses at length about how the vouchers were stored, handled and audited after they were turned in by Barron in late 1983. Even the storage box was repeatedly presented to witnesses for identification.

"I know you've busted your britches to bring this case to trial," Noble told prosecutor Maher as he entered a finding of not guilty on two of the charges late Friday. "But I'm a little concerned that the government has not analyzed what you're charging in this case . . . . The Army chose this extraordinary means to circumvent accountability for money. And it did it for a reason: specifically to cut off the ability to find the source of the money.

"And [in so doing] they also chose to risk losing the money . . . and they cut off statutory and regulatory claims against them . . . . You're hard-pressed, Capt. Maher, to show that a mechanism for a claim exists, even that a claim exists," Noble said.

Addressing the larceny charges, Barron's military lawyer, Capt. Joseph A. Woodruff, told the jury that the government had been unable to say how much money Barron was advanced and therefore to prove he had stolen any.

Barron denied he stole government funds, testifying that mistakes in his accounting for advances were due to his frequent travel and his failure to keep accurate records of his expenses -- partly "not to leave a trail" of his undercover activities.

"Somebody's got to be held responsible for this mess," Woodruff told the jury. "But the only problem is, the only person you have before you is Ramon Barron.

"We've had general officers testified about and high-placed Defense Department civilians testified about in this case . . . . Where's the responsibility going to be placed? Are we going to go to the bottom of the totem pole? Is that where the ax is going to fall? On the lowest-ranking guy in the whole outfit?"