The former employees allegedly mined Twitter data for information about critics of the Saudi regime, the Washington Post reported.
One of the former employees, Ahmad Abouammo, a U.S. citizen, was arrested on Tuesday, the report said.
The second, Ali Alzabarah, a Saudi citizen, allegedly accessed personal information on more than 6,000 Twitter accounts. He remains at large.
A third individual, who was not a Twitter employee, acted as an intermediary between the pair and Saudi government officials. That person, Ahmed Almutairi, was also charged in the complaint.
The case has also been linked to an associate of Saudi Crown Prince Mohammed bin Salman, who is believed to have ordered the murder of Jamal Khashoggi, a journalist and critic of the Saudi regime, last year in Istanbul.