The announcement came after Western environmentalists first exposed the issue, in the latest salvo of a battle that pits Japan against many of its usual allies, such as Australia and New Zealand.
An official at Japan's health ministry said whale meat was subject to extensive routine tests before and after import.
"We conduct strict checking because whales tend to collect contaminants in the environment such as pesticides and heavy metals," he said
He added that tests on Norwegian whale meat imported in April showed 0.2 parts per million of aldrin and dieldrin combined, in addition to 0.07 ppm of chlordane. Meat that arrived in June was found to have 0.2 ppm of dieldrin.
Japan's safety limits for the pesticides are 0.1 ppm for aldrin and dieldrin combined, and 0.05 ppm for chlordane, the official said.
In both cases the order was given for the contaminated meat to be abandoned, ministry data showed.
The official said such discoveries have not led to a halt or a scaling down of imports from Norway. He noted that imports from Norway have increased in recent years, but did not give detailed figures.
"There are very few countries where people still consume whale meat, so the food products are traded among those few countries," he said.
Grethe Bynes from the Norwegian Food Safety Authority said in-country tests on whale meat showed "only low levels".
"As we see it, it is safe to eat whale meat in Norway," she said.
The issue was raised by activists at the Environmental Investigation Agency and the Animal Welfare Institute, who also said international trade in the mammal's meat was being artificially stimulated.
"Norwegian demand for whale meat has fallen in recent years," the groups said in a statement.
"To boost domestic sales, and with an eye on new export markets, both the Norwegian government and its whaling industry are subsidising research, development and marketing of new whale-derived products."
Japan has used a legal loophole in the International Whaling Commission's (IWC's) 1986 whaling ban that allows it to continue slaughtering the animals ostensibly to gather scientific data.
But it has never made a secret of the fact that the whale meat from these hunts often ends up on dining tables.
However, consumption of whale meat in Japan has steadily and significantly fallen in recent years and there is little support for whaling itself, although a confrontational campaign by animal rights activists has galvanized some support for the practice.
Japan cancelled its 2014/15 Antarctic whaling hunt for the first time in more than a quarter of a century after a UN court ruled last year that the
programme was a commercial activity disguised as science.
Iceland and Norway issue commercial permits under objections or reservations registered against the IWC's whaling ban, and together catch
hundreds of whales per year.