Transportation Department supervisors ordered 50 employes yesterday to submit urine samples for drug testing, implementing for the first time President Reagan's year-old executive order on a drug-free work place.

All the random tests were conducted in Washington, and no refusals were reported, according to Melissa J. Allen, deputy assistant secretary for administration.

The department, under intense scrutiny because of public dissatisfaction with airline service and safety, is the first civilian department to begin random testing to detect the presence of traces of marijuana, cocaine, opiates, PCP or amphetamines in the urine of its workers.

Traces of marijuana can be detected in some individuals for days or weeks after it is smoked. Test results will be available in five to seven days, Allen said.

"It is our belief that random testing is the most effective way possible to help ensure that the Department of Transportation's safety and security employes are drug-free," Transportation Secretary Elizabeth Hanford Dole said in a prepared statement.

Kenneth T. Blaylock, president of the American Federation of Government Employees, branded the tests humiliating and unconstitutional. He urged the administration to call off urinalysis until the Supreme Court rules on its constitutionality.

Yesterday's 50 employes were selected by a laborious process that began when 30,000 of the department's 60,000 civilian employes were designated as holding safety-related or sensitive positions. The jobs ranged from driving a car for the department to handling air traffic, from handling top-secret papers in department headquarters to conducting safety inspections.

A computer randomly selected about half the department offices in the country and then randomly provided 5,000 names of employes nationwide who work in sensitive jobs in those offices.

Another computer run produced the names of 10.5 percent of the 5,000 names, and 50 of these individuals turned out to have been given the appropriate notices and to work in Washington.

Supervisors called the 50 employes about 45 minutes before the tests began.

Summoned employes from the main department building trooped over to the Coast Guard headquarters clinic in 15-minute intervals. Others reported to "designated bathrooms," Allen said.

At each site, they were met by two representatives of the Upjohn Co., one man and one woman, hired by the department to handle the sample-collection process.

Test takers identified themselves with photo I.D. tags and were asked about use of medicinal drugs that might show up on the tests.

The employe produced the sample in a closed stall where the water in the toilet has been dyed blue to prevent it from being used to dilute the sample.

The temperature of the sample was immediately taken, and must be within the range of 90 to 99.8 degrees, normal internal body temperature.

The bottle was covered with a tamperproof wrap and signed by the employe, then sent by express mail to CompuChem Laboratories in North Carolina for analysis. Each test costs $26 under the department's contract with the firm.

Dole said any employes discovered to be using drugs will be reassigned and allowed to enter a rehabilitation program.

John Thornton, president of the National Association of Air Traffic Controllers, said air traffic controllers were not tested yesterday because they have not received all the required notices. Thornton said that he expects random tests to begin Sept. 21. Controllers have been tested since February in connection with their annual physical examinations.

Although the military has been conducting random drug tests for several years, the Transportation Department civilian program is unique in its scope.

Under a congressional compromise worked out in June, other departments and large agencies must begin testing simultaneously after the public is given an opportunity to comment on the testing procedures, the total costs are reported to Congress and other steps are taken.

The June compromise exempted Transportation and a number of agencies from the all-begin-at-once rule. These are the Central Intelligence Agency, Bureau of Prisons, Drug Enforcement Administration, Federal Bureau of Investigation, Immigration and Naturalization Service, Army civilian workers, the Customs Service, the Bureau of Alcohol, Tobacco and Firearms, and the Secret Service.

Most of these agencies conduct drug tests when they have reasonable suspicion to believe that drugs might have been used and may begin random testing soon. The administration is trying to implement random drug testing virtually government-wide by year's end.