The U.S. Customs Service said yesterday that 16 of its employes are facing criminal charges, two have resigned and eight others are still under investigation in connection with Operation Clean Sweep, a year-long internal investigation of corruption at the agency.

In announcing the operation, Customs Commissioner William von Raab said that almost all the cases involve bribery and that most are drug-related.

The best-known case involves Jose A. Barron Jr., a border inspector at San Ysidro, Calif., who was arrested there May 4 after he allegedly allowed two pickup trucks to cross from Mexico without inspection. The trucks were found to contain 3,000 pounds of marijuana.

Subsequent searches of his house and his parents' house produced $640,000 in cash hidden in safes. The government has charged that Barron received $40,000 for each vehicle full of marijuana that he allowed across the border.

On June 1, Customs Inspector Leonard A. Lombardo Jr. was arrested at a motel in Jersey City and charged with the sale and distribution of cocaine. The arrest was made after undercover agents had made five purchases of cocaine from Lombardo, Customs said.

Von Raab said the investigation was conducted by 50 agents in eight teams across the country.