They were confirmed after additional sample tests were done at the National Public Health Surveillance Laboratory, Health Vice Minister Ausra Bilotiene-Motiejuniene told a press conference on Wednesday.
"We have to cases confirmed by laboratory tests," she said.
Both cases are imported, the vice minister said, adding that "we are speaking about the Czech Republic". They were confirmed after a group of four suspected samples were tested, and the samples came from Vilnius County. All contacts have been identified, she said.
Bilotiene-Motiejuniene says people will be advised to avoid large gatherings, evaluate which events or meetings could be postponed, wear masks, respirators and, if people develop symptoms, they should register immediately and arrive at mobile testing points for tests.
"This variant is four times more infectious. (…) People who had the jab 4-6 months ago, should consider getting the booster jab," she said.
Participants of the press conference could not say yet whether the Omicron-infected people had been vaccinated or not.
More suspected samples are now being tested and the results are expected on Thursday. The samples arrived from different cities, they said.
The highly-mutated coronavirus variant was first detected in South Africa last month, leading to bans in many countries on any travel from South African countries, as well as the reintroduction of internal restrictions to slow the spread of the new variant.
Experts warn Omicron spreads way faster than the now-dominating Delta variant, with lower vaccine efficacy being one of the reasons. Based on initial data, however, the new variant causes milder symptoms.