Pregnant women undergoing prenatal genetic testing should receive genetic counseling so they can make informed decisions. We examined the current state of providing genetic counseling in Japan to pregnant women before they elected amniocentesis for prenatal diagnosis of chromosome abnormalities and after test results were completed, and explored the opportunity for expanding access to certified genetic counselors (CGC) at clinical practices offering amniocentesis. An anonymous survey was mailed to the 298 hospitals that referred amniotic fluid specimens to LabCorp Japan in 2009. Most genetic counseling was provided by the obstetrician alone; 73.8 % (76/103) of pre-amniocentesis, 82.5 % (85/103) if normal results, and 49.4 % (44/89) if abnormal results. Respondents spent limited time in genetic counseling; 57.3 % spent <10 min for pre-amniocentesis, 88.3 % spent <10 min for normal results, and 54.0 % spent <20 min for abnormal results. While 45.8 % indicated that CGC do not have an essential role in clinical practice, responses that supported employment of CGC were more likely to come from hospitals that submitted more than ten specimens annually (p < 0.0001), university hospitals (p < 0.0001), and MD geneticists (p = 0.020). Currently, there is limited genetic counseling available in Japan. This indicates there are opportunities for the employment of CGC to improve the quality of genetic counseling.