The World Health Organization (WHO) considers carbapenem-resistant organisms (CROs) to be critical-level pathogens. Regular screening for high-risk CRO colonization is essential, especially in the ICU. Direct detection of carbapenem-resistant genes is possible using the FDA-approved Xpert Carba-R assay. This study evaluated its reliability compared with the culture technique at a tertiary hospital in Indonesia. A high number of CRO colonization was found using the culture technique and the Xpert Carba-R assay with about 31 and 26 positive results out of 100 total samples, respectively. Both methods detected bla_NDM in 11 samples, and the Xpert Carba-R assay detected one sample co-presenting with bla_VIM that was not detected by PCR. The Xpert Carba-R assay did not detect the gene in 73 samples following negative results with the culture technique. Fifteen samples were detected gene by the Xpert Carba-R assay though there was no gene by the culture method, showing that the Xpert Carba-R assay demonstrated a high degree of sensitivity in identifying carbapenem-resistance genes. Carbapenem-resistance genes common in Indonesia other than those examined by Xpert Carba-R assay in this study (i.e., bla_OXA-23 and bla_OXA-24) or non-enzymatic mechanisms may also produce resistance in many colonies without the examined genes. Finally, the Xpert Carba-R assay produced faster findings than the culture technique.