Introduction: The Non-Invasive Prenatal Testing (NIPT) guideline was issued and applied in 2013 by the Japanese Medical Association. Since being issued, the NIPT practice in Japan still has some problems related to indication, access, cost coverage and uniformity. Therefore, our study aimed to identify the Japanese challenges of adopting NIPT into prenatal diagnosis by comparing the system and process with other countries. Method: The United Kingdom, Germany, Italy, Sweden, and Taiwan were purposefully selected for comparison. All the countries, including Japan, introduced NIPT. The literature and information searches were conducted using PubMed, SCOPUS, Google Scholar, CiNii and Google searching engine. Results: The process of NIPT in Japan was very different from the other countries. Japan is the only country that indicated NIPT for only pregnant women over 35 years old in certificated facilities and did not have a policy regarding providing information on prenatal screening and NIPT to all women. Japan also did not have a policy regarding abortion due to fetal abnormalities. The practice of NIPT guidelines is different between non-certified and certified facilities. NIPT fee was the highest in Japan and was not covered by insurance. Conclusion: Pregnant women in Japan suffered from disparities in information access, economic burden, geographic location, and practice of NIPT guidelines between the certified and the non-certified facilities. Pregnant women-centered prenatal diagnosis policy, including NIPT, should be established in Japan by learning cases from other countries.