The Metro Transit and District of Columbia police continued their joint investigation yesterday of two reported mugging incidents that occured within 90 minutes of each other at Metro subway stations Friday night.

At the same time, they stressed that the Metro system has an extraordinary security record. The two muggings Friday were the first reported in stations in the 2 1/2-year existence of the subway system.

Angus B. MacLean, chief of the transit police, said that "statistically, the rate of incidents on the subway is quite low, but we know that if you are the victim you are not comforted by statistics."

For all of 1978, MacLean said, a total of 344 criminal offenses were reported to transit police and there were 238 arrests on or near subway property. In none of those cases was anyone actually beaten, MacLean said.

Of the 344 offenses, 20 were listed as assaults and 27 as robberies, including purse snatchings or pickpocket activity. Most of the remainder of the incidents ranged from disorderly conduct to playing a radio on the train. There were seven auto thefts from Metro parking lots.

Friday night, Mark Eisen, 24, of Springfield, told police he was struck on the head with a hard object and robbed of $50 while on the escalator at the Foggy Bottom station. Ninety minutes later, Bernard Livingston, 42, of Southwest Washington, was punched in the mouth and relieved of $7 while leaving the Deanwood station, he told police.

D.C. and Metro police share responsibility for the stations. Deputy D.C. Police Chief Robert Klotz said yesterday that "it has been my experience that Metro is secure; if these incidents had been commonplace, they would not have generated the news media attention that they have."