As of December 2023, there are 5 types of cancer gene panel tests covered by public insurance in Japan. Four of them partly feature companion diagnostics. When cancer gene panel test is used for the purpose of comprehensive gene profiling (CGP), a total of 56,000 points(44,000 points for the test administration fee and 12,000 points for the expert panel fee) can be claimed, whereas if the cancer gene panel test is used for the purpose of companion diagnostics, hospitals can claim only the reimbursement as a companion diagnostics, which fee is much cheaper than that of CGP. Therefore, cancer gene panel tests are rarely used as a companion diagnosis in daily clinical practice. Even when the test is performed as a CGP test, since its indication is limited to patients who have completed or are expected to complete standard chemotherapy, most biomarkers associated with approved drugs are already evaluated with stand-alone companion diagnostics at the time of CGP test application. On the other hand, there are some approved drugs, such as pembrolizumab for TMB-H or entrectinib or larotrectinib for NTRK fusion gene, for which there is no stand-alone companion diagnostics and the eligibility for these drugs cannot be judged without the results of CGP test. This paper discusses the current status and issues of companion diagnostics in cancer genomic medicine.