"Overall, we have five cases, three of which are imported," Daiva Razmuviene of the National Public Health Center (NPHC) told BNS on Friday.
"In one case, the source of infection is being investigated, and the remaining one has been traced to a person who has [recently] been abroad," she said.
The patients, aged between 26 and 46 years, have developed symptoms, but none are in hospital, according to the epidemiologist.
Lithuania detected its first two Omicron cases earlier this week.
The highly-mutated coronavirus variant was first detected in South Africa last month, leading to bans in many countries on travel from South African countries, as well as the reintroduction of internal restrictions to slow the spread of the new strain.
Experts warn Omicron spreads much faster than the now-dominant Delta variant, with lower vaccine efficacy being one of the reasons. Based on initial data, however, the new variant causes milder symptoms.