We wish to respond to a Commentary article by Nicholas J. Gales and colleagues, “Japan's whaling plan under scrutiny” (Nature 435, 883–884; 2005).

The title of the article inappropriately uses the term “whaling”. Research on whales is conducted according to provisions of the International Convention for the Regulation of Whaling (ICRW) and is fundamentally different from commercial whaling.

It is true that the government issuing research permits may determine the sample size, and there is no requirement to change this on the advice of other governments. But Japan has submitted annual research plans to the Scientific Committee (SC) of the International Whaling Commission (IWC) for review and has incorporated amendments following any constructive suggestions from the SC. Gales and colleagues present their negative criticism of Japanese research as if this was the opinion of the SC. However, many positive comments have been made and reported by the SC over the years.

The authors condemn Japanese research on the basis of the number of whales captured since 1987. In planning our research, we must carefully determine the sample size that can achieve statistically valid results while also safeguarding population levels. Any criticism should address the rationale for calculating sample size, not merely highlight a number that seems large. Our research proposal describes this process clearly.

Criticism that science is being used as a cloak to hide the purpose of killing whales is inappropriate. The lethal method used for sampling is required to achieve our research objectives, including determination of age and detailed data on stomach contents. Also, parts of Japan's research programme use non-lethal techniques for sighting surveys and oceanographic studies, as well as biopsy sampling.

Contrary to the authors' comment that the publication record of our 18-year research programme is “very poor”, we have made more than 150 scientific papers available to the SC and had a further 79 published in academic peer-reviewed journals. Unfortunately, many journals reject papers that report data from lethal whale sampling, even though they accept papers on other lethally sampled mammals.

In January 2005, the government of Japan held a meeting to review data and results from the previous 17 years of research (JARPA) in order to assist the planning of the new research programme (JARPA II). Many anti-whaling scientists, including the authors of the Commentary article, chose not to attend, although every member of the SC was invited. The Commentary claims that Japanese whale research is being conducted in an area designated as a sanctuary by the IWC. But the creation of this sanctuary was not recommended by the SC, and it was designed only to protect whales from commercial whaling.

Our new plan for Antarctic whale research (JARPA II) has been designed with far-reaching objectives to ascertain the dynamics of the Antarctic ecosystem. The Commentary authors say this is a job for the Commission for the Conservation of Antarctic Marine Living Resources, but this organization does not conduct research on whales; Japan plans to collaborate with it to achieve JARPAII's research objectives. Japan has provided skilled labour, logistics and vessels to the IWC for large-scale Antarctic whale surveys conducted with multinational researchers.

Research of the magnitude of JARPAII is costly. Funds may be obtained by selling the by-products of whale research, according to Article 8 of the ICRW. Critics who say this makes the research a commercial enterprise are denying a provision of the ICRW.

Finally, the Commentary was written and published using information from the SC that, under IWC rules, should have remained confidential until the IWC's opening plenary session on 20 June.