Since its inception in 1987 the ICR had whale research under special permit as the core activities of the Institute. The whale research program in the Antarctic (JARPA) started the year the Institute was established and its second phase began in 2000. The research program in the western North Pacific (JARPN) was launched in 1994 and expanded to its second phase in 2005. Thereafter, the Institute had been conducting the New Scientific Whale Research Program in the Antarctic Ocean (NEWREP-A) which was launched in 2015, and the New Scientific Whale Research Program in the western North Pacific (NEWREP-NP) since 2017. The whales captured in these surveys should be effectively utilized according to the International Convention for the Regulation of Whaling regulations (Article VIII Paragraph 2) which require that research byproducts be processed and utilized as far as practicable. Thus, the whale research byproducts were sold within Japan under the guidance of the government, and the proceeds of the sale were used to cover a portion of the cost of the next surveys.
In the sale of these byproducts, the Institute, under the guidance of the government with the advice and support of various organizations, made always efforts to ensure that they spread widely to the public. Both NEWREP-A and NEWREP-NP research programs ended with the resumption of commercial whaling on 1 July 2019, and the sale of research byproducts ended in March 2020.