this took place off the Kurile Islands (as the Russians call it), aka the Northern Territories (as the Japanese call it).
the CNN report is a bit naughty in not mentioning this fact until the very end of its report, and using the euphemism "east of Japan's northernmost main island of Hokkaido" in the opening paragraph.
ownership of the Kuriles/ Northern Territories have been disputed by Japan and Russia since the end of WWII (and indeed, it's because of this dispute that Japan and Russia still haven't signed an official peace treaty to conclude WWII). recently, Putin has been promising to increase investment in the Kuriles - allegedly because it's shockingly run-down, even by Far East Russian standards (no-one disputes this is fact, by the way), but most likely to guarantee ongoing Russian possession of the islands.
clearly Japanese fishing fleets have been trawling in the waters of the Kurile on the basis that they're really Japanese islands - which would be why the fishing boat didnt turn tail and leave when challenged by the Russian coast guard; equally clearly the Russian authorities have decided to make a public stand about their claims to the Kuriles - which is why they've started shooting ppl.