A 29-year-old assistant U.S. attorney, known as bright and personable and a "tough prosecutor," was arraigned today on charges of stealing heroin and cocaine worth $450,000 from a safe where it was being held as evidence in federal narcotics trials.

Daniel Perlmutter, a Phi Beta Kappa graduate of Williams College and a former editor of the New York University Law Review, was arrested by FBI agents early this morning at a downtown coffee shop with his girlfriend, Stacy Honeycutt, an unemployed actress.

Both were charged with three counts of narcotics possession with intent to distribute and with theft of government property. Each now faces a maximum sentence of 45 years.

Ronald P. Fischetti, Perlmutter's lawyer, said both will plead not guilty to the charges in a bail hearing set for Monday. Perlmutter is being held in preventive detention until then; Honeycutt was released on a $25,000 personal recognizance bond.

U.S. Attorney Rudolph W. Giuliani, who represented the government before U.S. Magistrate Harold J. Rabey today, said the case has had "a devastating impact on the morale and sensibilities and feelings in this office." His staff of 131 lawyers is one of the nation's largest.

Giuliani, a former associate attorney general, has maintained a high political profile in New York and is reportedly considering a run for elective office, against Gov. Mario M. Cuomo or Attorney General Robert Abrams.

In an interview, Giuliani described Perlmutter as an "engaging, nice" person and "one of the most productive, hard-working, hard-driving guys -- a tough prosecutor, a guy you would not want to be investigated by." A native of New Brunswick, N.J., Perlmutter has been an assistant U.S. attorney since March 1983, and earns $41,000 a year in the narcotics division.

Giuliani said Perlmutter began to suffer "psychological and emotional problems" after he split up last December with his wife, an assistant U.S. attorney in Newark. Later, Perlmutter's friends say, he became involved with Honeycutt, 22, a New Brunswick native and fine-arts graduate of Rutgers University.

Giuliani said the investigation began Sunday night when two prosecutors, preparing for trial, found that their evidence -- including 8.7 ounces of heroin and 29.2 ounces of cocaine -- was missing from a safe on the third floor of the U.S. attorney's office.

Giuliani was contacted immediately and the Federal Bureau of Investigation was brought into the case, he said.

Perlmutter was not one of the four persons authorized to have the safe's combination, according to Giuliani. But after the couple was arrested, he said, agents searching their Park Avenue apartment found in a wastebasket a scrap of paper with the combination on it.

Also found were Drug Enforcement Administration bags, one containing a white, powdered substance, another with powder residue; a glassine envelope containing white powder, financial records and drug paraphernalia, including equipment pipes, filters and a "free-basing bowl," Giuliani said.

At his arraignment today, Perlmutter smiled frequently and kissed Honeycutt as he was led away in handcuffs.