Fergus Ewing said proposals in the Fisheries Bill would allow UK Government ministers to set quotas for fishing in Scottish waters, claiming this came "despite assurances that this is not their intention".
He added: "The UK Government has failed to adopt the amendments we provided to ensure that Scottish fisheries are still managed by Scottish ministers.
"As with much of Brexit, it appears that once again the UK Government is ignoring the settled devolved process."
He said ministers at Holyrood will "resist any measure which shifts responsibility for any devolved aspect of fisheries away from Scotland".
The Bill, introduced at Westminster on Wednesday, will end the current automatic rights for EU vessels to fish in British waters.
UK Environment Secretary Theresa Villiers said: "This new Fisheries Bill takes back control of our waters, enabling the UK to create a sustainable, profitable fishing industry for our coastal communities whilst securing the long-term health of British fisheries."
The Bill contains a legal requirement for all fishing to be carried out at "sustainable levels", and sets out for the UK Government and devolved administrations to "co-ordinate fisheries management where appropriate".
UK fisheries ministers George Eustice said: "The Fisheries Bill gives us the powers to implement our own independent fisheries policy, improve our marine habitats and make decisions based on the health of our fish stocks, not vested interests.
"For many people in coastal communities, taking back control and leaving the Common Fisheries Policy is at the heart of getting Brexit done, and this Bill delivers for the environment, fishermen and the union."
But Mr Ewing said ministers in Edinburgh are "seriously concerned that Scotland still does not have its own place at international fisheries negotiations as a matter of right, something that we have long called for".
He added: "We still have no clarity nor certainty over future funding to support future investment in our fishing industry, despite pressing for this over the last three years."
The UK Government said the Bill fully respects the devolution settlements and that it had worked closely with the devolved administrations, including the Scottish Government.