Joji Morishita said the whole debate about whether or not Japan should be killing the mammals had long since moved away from science and into politics.
The scientific committee of the International Whaling Commission said in a report Friday that Japan had failed to give enough details to explain why it wanted to kill almost 4,000 minke whales in the Antarctic over the next 12 years.
Despite international disapproval, Japan has hunted whales in the Southern Ocean under an exemption in the global whaling moratorium that allows for lethal research.
"There is no definite conclusion in the report itself... which is not so surprising in the IWC, because as we know very well the IWC is a divided organisation," Morishita told reporters.
"Because of this division, even the scientific committee is always having difficulty in coming up with some kind of a conclusion.
"Still... We will try to provide as much scientific research as possible and try to get" approval from the scientific committee for their go-ahead.
Asked whether Japanese ships would hunt in the Southern Ocean later this year, he said Tokyo's position had not changed since an announcement on Friday.
But he added: "Without finishing those additional analyses, I don't think it is appropriate to say whether we will start our research activity from this winter or not."
Japan does not need permission from the IWC to press on with its "lethal sampling" hunt in December, because it is ultimately up to individual countries to issue permits for whaling on scientific grounds.
Japan believes the world's whale population, especially the minke stock, is sizeable enough to accommodate a return to sustainable whaling, putting it at odds with campaigners and anti-whaling nations.