We examined the molecular characteristics of 13 phenotypically confirmed carbapenemase-positive Enterobacteriaceae clinical isolates, including the relationships between plasmid-mediated quinolone-resistance genes (qnr), 6'-N-aminoglycoside acetyltransferase-encoding genes [aac(6')] and AmpC-encoding genes (pAmpC). Twelve isolates were bla(IMP-1) positive (92.3%), while one was bla(IMP-11) positive (7.7%). We detected qnr, aac(6') and pAmpC genes designated bla(ACT-1)-like in 76.9%, 100% and 53.8%, respectively, of the 13 isolates. Plasmids were transferred successfully for three of the 13 metallo-β-lactamase (MBL)-producing isolates, and the sizes of plasmids extracted from these donors and transconjugants were deduced to be 65 kb or 70 kb. OmpC or OmpF protein expression was reduced in all Enterobacter cloacae, and one Klebsiella oxytoca lacked OmpK36. We demonstrate what appears to be the first evidence that, in Japan, Enterobacteriaceae producing MBLs carry various plasmid-mediated resistance genes, which may cause a further decrease in carbapenem susceptibility through reduction of the expression of outer-membrane proteins.