Many fishermen are hostile to Europe, with a poll before the referendum suggesting that as many as 92% could vote to quit the European Union (EU).
Meanwhile, the Scottish Government has been making the case for Scotland to retain its links with Europe after more than three out of five voters north of the border opted to remain.
Although the UK voted to leave, Mr Ewing said key fishing talks would continue over the minimum two-year period needed for Brexit negotiations.
He said: “I am working with the fishermen’s representatives, I respect their views, I understand they have a different perspective from the Scottish Government, but that will not stop us working constructively to get the best deal for Scotland.
“Of course we’re going to remain in the EU for at least two years, no matter what happens, that’s two years minimum of negotiations, of December fisheries councils, and I for one will approach those negotiations from a standpoint of having had in-depth meetings with fishermen’s representatives in order to understand their case and best advance it.”
The Rural Economy Secretary added: “We’re doing our day job, we’re getting on with representing Scotland’s fishermen, now and in the big picture of what may happen later.
“Of course there is the fishing fleet where I understand that there is substantial support for leave, and we must understand their viewpoint.
“But also part of the fishing sector is the onshore sector, the processing sector, where many of the workforce are not originally from Scotland, and I believe nearly £500 million of fish is exported to the EU.”
As well as meeting leading figures from the Scottish Fishermen’s Federation, Mr Ewing also met workers at the Scotbeef meat processing plant in Glasgow, where almost half the staff come from other parts of Europe.
He told employees from Poland and the Czech Republic: “We think people who work hard in Scotland should be able to stay here.”
Scottish firms export £724.3 million of food and drink to other parts of Europe, making the continent the largest destination for produce from this sector.
Mr Ewing said: “Scotland’s food and drink industry is one of our economic success stories and our quality produce is known and loved at home and abroad. Our place in the European Union has been key to that success and we must protect it.
“Workers from around Europe are employed in many of our food and drink businesses and I want to reassure them that we value and welcome the role they play in our country - both economically and in terms of civic vibrancy.
“Europe is also a key destination for much of our food, with exports worth a total of £724.3 million in 2015.
“It is clear that European workers and exports are crucial to the food and drink industry and to our economy.
“I am committed to helping the First Minister protect our place in Europe and calling for immediate guarantees about the residency status and other rights of those from around Europe that have chosen to make Scotland their home.”