Tense relations between the Scottish Government and the country's largest fishing industry body, the Scottish Fishermen's Federation, have hit a new low after the First Minister delivered a stinging public rebuke to its leader.

SFF chief executive Bertie Armstrong, who has characterised relations between the skippers' association and the Scottish Government as "creative rough and tumble - like any trade association holding government to account", wrote to Alex Salmond on May 12, seeking clarification on reciprocal rights of access to Scottish and Norwegian waters raised by the First Minister's Bruges speech of April 28.

Armstrong said that Salmond was "playing the man, not the ball" instead of satisfying due diligence on behalf of SFF members.

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In his speech to the College of Europe in Belgium, Salmond said the "alternative" to smooth Scottish accession to EU was "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".

Armstrong wrote: "You indicate that should Scotland find itself outside the EU, the transit of EU fishing vessels through Scottish waters to Norwegian zone will be prohibited. That would be contrary to the principle of innocent passage laid down in the law of the sea - will you explain what you meant?"

In a response which was posted by the SFF on its website last week, the First Minister lashed out at Armstrong, accusing him of a "ridiculous interpretation" of his speech, hinting that the "astonishing" line of questioning followed the lead of Tory Scottish Office minister David Mundell MP, as quoted in an article in The Herald.

Salmond goes on to explain that he was not threatening that an ex-EU Scotland would bar continental fishing boats from passing through Scottish waters, but instead that he meant that extracting Scotland's from the EU would force a recalibration of complex swap arrangements previously negotiated between the EU and Norway, a non-EU state.

The First Minister claims this would lead to a "drastic reduction in their quota opportunities in Norwegian waters as a result of losing Scotland's contribution to this exchange". But fisheries experts questioned if removing Scotland from the EU quota system would have more than marginal effect on longstanding bilateral swap arrangements between, say, Spanish and Norwegian fishermen.

The spat threatened to degenerate when, during a Scottish Parliament debate on the findings of the European and External Affairs Committee's report on Scotland's EU membership, SNP Aberdeen MSP Maureen Watt accused Armstrong of being "on a sticky wicket, because he's not maintaining the impartiality that an employee of the Scottish Fishermen's Federation should do".

Watt said that the remark, in a response to a question by Labour MSP Lewis Macdonald about the bargaining power of smaller EU members, followed Armstrong's public grilling of Scottish Government Fisheries Minister Richard Lochhead at an onstage Q&A at the Scottish Skipper Expo, an industry conference in Aberdeen last week.

Armstrong had asked Lochhead to cite examples of when the interests of the Scottish fleet had been "sold down the river" by the UK Government's Department for Environment, Food & Rural Affairs (DEFRA).

The fishermen's leader has denied any political bias in the undertaking of "due diligence" on potential constitutional change from Scottish and UK Government ministers, and the opposing referendum campaigns.

He cited identical open letters to both governments and referendum campaigns seeking factual guidance for fishermen on complex issues surrounding the effect of a Yes or No vote on fishing rights, landing quotas, and ownership of the seabed.

Armstrong said: "I wasn't sure what the First Minister meant so I asked him the questions. It's pretty simple stuff. There was no need to poke me in the eye as a result.

"Similarly with Maureen Watt, she didn't answer the question, instead she attacked me, although we have since discussed the matter and cleared the air.

"I offered assurance that the SFF's function throughout the referendum discussions is to ask questions akin to the business process of due diligence. I have a mandate to ask those questions and none to offer opinions. We explored the issue surrounding the pursuit of undoubtedly difficult inquiries during the referendum period; whatever way they are phrased or caveated they may sound to some as implied criticism or impartiality."

Richard Lochhead's office said that he would be responding to the other five questions on the EU from the SFF "shortly".