They're not though, the catch is for scientific purposes, so they take only the 500 or so that they need for research each year, then onsell the meat rather than wasting it.
I have actually found a paper by a Japanese research institute that obtained its samples from the Nisshin Maru:
Habitat and prey selection of common minke, sei, and Bryde’s whales in mesoscale during summer in the subarctic and transition regions of the western North Pacific
Their methods section is a bit vague though:
We conducted surveys of oceanographic observations and whale prey species from on board the R/V Shunyo Maru (887 GT, National Research Institute of Far Seas Fisheries) in the western North Pacific from 21–25 July 2008 and 10–22 July 2009 (Fig. 1). These surveys were conducted concurrently with whale sighting and sampling surveys as part of JARPN II by researchers on the Nisshin Maru (7575 GT, Kyodo-Senpaku Co., Ltd.) and two sighting/sampling vessels (Yushin Maru No. 2 and No. 3, 742–743 GT, Kyodo-Senpaku Co., Ltd.) on the same survey track lines during daylight periods from 1 h after sunrise to 1 h before sunset. In 2008, we conducted a survey of Bryde’s whales within a survey area bounded by 35–39°30′N and 146–148°E, where the SST ranged from 17.5–27.6°C (Fig. 1). In 2009, surveys of common minke and sei whales were conducted within an area bounded by 43–45°N and 154°30′–157°30′E (SST 10.2–14.7°C), and 39–41°N and 156–160°E (SST 14.9–18.8°C), respectively (Fig. 1; Table 1). According to previous reports [1, 11, 12], these areas covered the southern part of the main distribution area of common minke and sei whales, as well as the main distribution area of Bryde’s whales, in terms of both latitudinal and SST ranges.
It's OK - they're just "surveying" the whales, just like ornithologists survey birds with a shotgun prior to roasting them