The Scottish Fishermen's Federation (SFF) met the UK environment secretary and fishing minister in London.
Talks with the Scottish government's Brexit minister Michael Russell were also held at Holyrood.
The SFF campaigned for a Leave vote in June's referendum, and argue Brexit could present an opportunity.
The organisation said control over British waters would bring huge potential benefits to Scottish fishing.
Research by the North Atlantic Fisheries College said only 42% of fish caught in these waters between 2012 and 2014 were landed by British fishermen.
The other 650,000 tonnes were caught by vessels from elsewhere in the EU.
The SFF's chief executive, Bertie Armstrong, said the UK's exit from the EU represented a ''sea of opportunity'' for the industry.
He told BBC Scotland: "When we joined the EU, our waters were turned over to common grazing.
"The end result after 43 years is that more than half the fish from our EEZ [Exclusive Economic Zone] is removed not in UK beneficial hands.
"No other coastal state would dream of doing that, so the chance to restore some equilibrium there to the big advantage and benefit of the UK industry will present itself."
Scottish Rural Economy Secretary Fergus Ewing and Scotland's Brexit Minister Michael Russell met the Scottish Fishermen's Federation at Holyrood.
Mr Ewing said that he had "reiterated" that Scotland must be treated as an equal partner in EU discussions.
He said: "I want to be the champion of the Scottish fishing industry which is why we are engaging closely with them and listening to their particular needs and concerns.
"It is important that we recognise the value of the EU as a market of fish products as well as providing vital funding through the European and Maritime Fisheries Fund."
Scottish fishing leaders have said they are "encouraged" by talks with the UK and Scottish governments about Brexit.