Becoming an independent country is a risk-free route to securing a better deal for Scottish fishermen, the Cabinet secretary for rural affairs has claimed.

Richard Lochhead MSP set out the case for a better deal for the Scottish fishing industry under independence in a letter to trade organisation the Scottish Fishermen's Federation (SFF), in response to a request for clarification from the SFF lodged almost two months previously.

The SFF's letter, a copy of which was also sent to UK fisheries minister George Eustice MP, asked for clarification on the practical effects of transition to independence or the status quo following the September 18 referendum.

In his response, Lochhead attacked the UK Government's stewardship of the Scottish industry, but failed to respond to SFF questions predicated on any but the most optimistic scenario of Scottish fisheries' negotiations with the European Union.

Lochhead also sidestepped the SFF's request that the Scottish Government "clarify for all the balance of risk and benefit", on the grounds that he "expected EU member states to be keen to see an independent Scotland effect a smooth transition to membership".

The SFF, headed by chief executive Bertie Armstrong, has expressed scepticism about the 18-month timetable for Scotland's transition to full EU membership after a Yes vote, calling it "a significant under-estimate" based on "our own experience of European negotiation and law-making, and with reference to all previous accessions".

However, Lochhead declined the SFF's invitation to define a worst-case scenario as well as the 18-month "best case", or to detail the "spread of possibilities for status in Europe regarding regulation and access to other member states' waters for an independent Scotland during negotiations on EU membership".

Belief that other European states would unanimously respond to Scotland's demands was, the Cabinet secretary said, based on the "significant strength" of the country's bargaining position. He said this would discourage European non-compliance with all of Scotland's wishes and the timeframe of putting these wishes into effect.

He wrote: "Scotland is the second biggest contributor to EU/Norway fish negotiations, and is at the heart of a delicate and complex access agreements involving 27 other countries from both within the EU and beyond."

He also cited the oft-quoted expert opinion from UK legal authorities that an 18-month time frame was "realistic".

Lochhead used his response to the SFF questions to launch a new attack one the UK Government's record on stewardship of the Scottish industry, saying that its negotiation of the Common Fisheries Policy had "caused untold damage to our fishing communities". He added that "it was difficult to conclude by any measurement that successive UK Governments have negotiated good deals in relation to fisheries funding".

He said that the new European Marine and Fisheries Fund, the framework allocation of European support for member states, "represents an extremely poor allocation given our share of EU landings",

In his response to the SFF questionnaire, Eustice asserted that "Scotland directly benefits from significant UK influence in Europe and a long standing track record of securing positive outcomes".

For his part, he cited the reformed EU Common Fisheries Policy, where the UK successfully secured a new model of decentralised ­decision-making which was a Scottish Government priority, plus the prevention of a cut in days at sea for Scottish fishermen, the increase in cod quota, and a deal on mackerel with Norway and the Faroe Islands.

He also mentioned the "regular participation of Scottish Government ministers in UK ministerial delegations to Brussels, and the day-to-day collaboration between fisheries officials in Defra and the Scottish Government."

Separately, the new Conservative MEP for Scotland, Dr Ian Duncan, has accused Lochhead of being "disingenuous in his remarks regarding the European and Maritime Fisheries Fund", given that Scotland's allocation from the fund rose during the recent negotiations and that SNP MEPs "made no comments, raised no issues, lodged no criticisms and made no attempt to amend the funding criteria of the regulations … despite the fact that one of your MEPs sits as a full member of the European Parliament's fisheries committee, and enjoyed unrivalled access to the drafting of the EMFF for which two SNP MEPs voted in favour."

SNP MEP Alyn Smith has accused Duncan of "clever-clever school debating society point scoring" on this issue, saying that he and fellow SNP MEP Ian Hudghton "supported the eventual compromise, in the same way as we accepted, on balance, the eventual overall EU budget. That did not preclude making numerous points in the negotiations as it was being produced."