The reason why cows carrying the mutation of complex vertebral malformation (CVM) show poor reproductive capability although they carry only one mutant allele is still not fully understood. Monitoring the progesterone profiles during oestrous cycle and early pregnancy in carrier cows might help explain their lowered reproductive capability. Progesterone concentration was measured in 19 CVM carrier cows and 21 control cows during oestrous cycle and early pregnancy. Milk samples were collected from all cows starting on the day of artificial insemination until day 45 post-AI. Progesterone was measured in skim milk using enzyme-linked immunosorbent assay (ELISA). Progesterone concentration was significantly reduced on day 7 (p < 0.05) and day 9 (p < 0.01) post-insemination in conceived CVM carrier cows when compared with that in control conceived cows. The mean progesterone concentration during early pregnancy was significantly lower (p < 0.05) in conceived cows with CVM than that of control cows in the same period. However, the mean progesterone concentration did not differ significantly (p = 0.072) in CVM cows that showed fertilization failure or embryonic death than that of control cows. Additionally, of 13 conceived control cows, eight cows (61.5%) showed normal luteal function. In contrast, of nine conceived CVM cows, only four cows (44.4%) showed normal luteal function. The conception rate was 47.4% in CVM carrier cows and 61.9% in control cows, but this difference did not reach significance. In conclusion, progesterone concentration might be lowered during early pregnancy in conceived CVM cows compared with that in control cows.