Objective: This study aims to assess the attitudes toward non-invasive prenatal diagnosis (NIPD) and NIPD problems in clinical practice in Japan. Methods: A mail-in survey using a self-reported questionnaire was conducted among pregnant women and health professionals. The questionnaire enquired about attitudes, concerns, and expectations regarding NIPD. Results: The responses from 252 respondents revealed that pregnant women have more positive attitudes toward NIPD than health professionals. In addition, there were wide discrepancies in concerns and expectations about NIPD, between medical professionals and pregnant women. The respondents with less NIPD knowledge had a more positive attitude toward the clinical application of NIPD. There was concern expressed by clinical geneticists whether an NIPD test should be performed or not when there is a lack of knowledge about the NIPD. All of the health professionals emphasized the importance of providing genetic counseling prior to and after the testing. Conclusion: Pregnant women place importance on the safety and non-invasiveness of the NIPD tests, whereas medical professionals consider the diagnostic accuracy and reliability of the test to be the most important. Health professionals pointed out that the tests might be frequently performed without the pregnant women having adequate knowledge or counseling.