Backgroud: A variety of open-system Real-time PCR (RT-PCR) assays for several acute respiratory syndrome coronavirus 2 are currently in use. The impact of omicron on the laboratories’ testing capacity is unknown. This study aimed to ensure the quality of omicron testing and to assess the comparability of cycle threshold (Ct) values derived from RT-PCR. Methods: Five external quality assessment (EQA) rounds using the omicron virus-like-particles were organized between February 2022 and June 2022 in Beijing, China. Results: A total of 1401 qualitative EQA reports have been collected. The overall positive percentage agreement was 99.72%, the negative percentage agreement was 99.75%, and the percent agreement was 99.73%. This study observed a significant variance in Ct values derived from different test systems. While interlaboratory using the same test system yielded comparable Ct values. Conclusion: There was strong concordance among laboratories performing qualitative omicron testing. However, caution is needed when comparing Ct values derived from the different test systems.