Richard Lochhead wants "radical changes" to the Common Fisheries Policy to give more control to local and regional communities.
He said Scotland has suffered years of "painful cuts and baffling rules imposed by the EU", including quota reductions which he blamed on irresponsible fishing by Iceland and the Faroe Islands.
He has also called for Scottish seafood to be sold at a premium, similar to Scotch beef and lamb, to reflect its "delicious and high-quality" status.
Reflecting on the challenges facing the Scottish fishing industry in 2013, Mr Lochhead said: "After years of painful cuts and baffling rules imposed by the EU, some progress was achieved last month at the Fisheries Council in Brussels meaning there is a chink of light for Scottish fishing.
"The key is to keep up the momentum for change as we prepare for more crucial decisions in 2013."
He said more can be done to "capture the value of fish landed on our shores".
"Scottish seafood is delicious and high quality, yet that is not always reflected in the price achieved for our fish and shellfish," he said.
"I believe we can secure a premium for Scottish seafood, much in the same way as is achieved for Scotch beef or Scotch lamb.
"The Scottish Government is committed to working with the industry in 2013 to help achieve that."
Mr Lochhead's immediate priority this month is to reach a positive outcome in the EU-Norway talks, including the cod and mackerel quotas.
"The excessive fishing of the mackerel stock by the Faroes and Iceland means a quota cut is expected for that fishery," he said.
"However, I will not accept a double whammy for our pelagic sector, and will therefore reject European Commission's proposals for an even greater quota reduction that only rewards Iceland and Faroes for irresponsible behaviour.
"We need the EU to confirm the long overdue sanctions and take action if Iceland and the Faroes continue to overfish."