Fisheries leaders have warned Alex Salmond that he risks a clash with the fishing industry after he claimed that 12 European nations could be barred from Scottish and Norwegian waters if an independent Scotland was refused EU membership.

In a keynote speech to the College of Europe in Brussels, the first minister said Scotland had much to offer the EU and called for a "practical, common-sense" approach to ensuring it inherited membership after leaving the UK.

But in a passage that has alarmed the fishing industry, Salmond warned that the alternative would be "the fishing fleets of 12 countries being denied any access to Scottish waters and, as a consequence, their access to Norwegian waters, which is also dependent on Scottish access."

One senior industry figure, who asked not to be named, said Salmond's words appeared to be a threat that "stokes considerable fear in our hearts".

David Mundell, the Scotland Office minister, said Salmond had made a significant legal and diplomatic error by threatening to block access to Norwegian waters. He said an independent Scotland would be legally obliged to allow safe passage to foreign ships with Norwegian fishing rights.

He said Scottish fleets fished heavily in other EU waters, including in North Sea areas owned by the rest of the UK.

"It has been a telling day for the first minister's judgment," Mundell said. "In the morning we read about his admiration for Vladimir Putin [the Russian president] and by afternoon he was threatening EU members with fishing ground blockades – the very members he would need to unanimously accept a new Scottish state. It has not been a masterclass when it comes to his diplomacy skills.

"The truth is, only a very small proportion of other member states' catches are taken from Scottish waters, and in any accession negotiations other member states would be more likely to press for improved access to Scottish fishing grounds in the North Sea than to make concessions for Scotland."

Bertie Armstrong, chief executive of the Scottish Fishermen's Federation, said he would be writing to the first minister asking him to explain what he meant.

"We need to ask the Scottish government for clarification of exactly what he means," Armstrong said. "Is this a threat to the rest of Europe or is fishing being placed on the table as a bargaining counter?"

He said that rhetoric would involve problems with the Spanish and Irish governments, in particular, but also raised questions about Scotland's rights to fish in other UK waters post-independence – effectively closing off large areas of the North Sea and Irish Sea.