Ross Finnie told the Scottish Parliament that the recommendation from European Union scientists was "politically unacceptable and economically ruinous".
And he said he was committed to finding "viable alternatives" to a complete ban on fishing for cod.
European Union scientists have proposed a total ban on cod fishing, the staple catch of the Scottish fleet, in an effort to conserve stocks.
Haddock and whiting catches could also be banned, because the larger cod are accidentally caught in the same nets.
Fishing industry leaders have questioned the research and have told Mr Finnie that the ban would mean the collapse of the Scottish fishing sector.
Opposition parties have pressed him to oppose the plan when he meets European ministers for quota talks.
In a hard-hitting statement, Mr Finnie told MSPs that action had to be taken - but closure was not an option.
Long-term decline
"I reject the wholesale closure of the Scottish fishing industry as politically unacceptable and economically ruinous for Scotland's fishing communities," he said.
"But the clear message from the scientists is that if we pursue business as usual, the day of reckoning will simply come later as white fish stocks continue their long-term decline.
"Doing nothing is not an option.
"I will not allow the destruction of the Scottish industry, nor will I see it destroyed in a few years' time because we did not respond to the long-term trend set out in the scientific evidential basis."
Mr Finnie said difficult decisions could not be ruled out.
"This is a hugely complex problem and we can only solve it in close collaboration with the industry," he said.
"We have already begin a series of meetings with them. It will require goodwill on the part of all concerned if they are to succeed.
"Emotions are understandably running high, but know that goodwill exists and together we will therefore construct a package of measures to prevent wholesale closure."
'Prepared to fight'
He said this package would have to win the support of other member states affected.
But he stressed: "I am committed to producing a sustainable future for the Scottish fishing industry and to finding viable alternatives to wholesale closure."
He added that action already taken in Scotland - such as a decommissioning scheme and the introduction of nets with larger mesh sizes - had to be taken into account.
Scottish Fishermen's Federation chief executive Hamish Morrison said Mr Finnie's statement was "more robust" than what had been heard until now.
"I think it is a relief that the minister seems to be prepared to fight for the best," he said.