The bottlenose dolphins were herded into a cove this weekend and their escape route was blocked by netting strung by fishermen who plan to slaughter the mammals for food.
The Sea Shepherd Conservation Society told CNN that two over-stressed dolphins had already died and would likely spend another long night in captivity.
The fishing industry in Taiji Cove considers dolphin harvests to be an acceptable historic custom and rejected criticism from outside Japan, including a condemnation by U.S. Ambassador Caroline Kennedy, CNN said.
"Taiji dolphin fishermen are just conducting a legal fishing activity in their traditional way in full accordance with regulations and rules under the supervision of both the national and the prefecture governments," a spokesman for the fishermen said. "Therefore, we believe there are no reasons to criticize the Taiji dolphin fishery."