Michael Gove has been accused by Scottish ministers of breaking Brexit campaign promises to protect rural funding from the EU worth hundreds of millions of pounds.

The Scottish government said Gove, the UK environment secretary, had refused to guarantee that £700m in funding for the country’s vulnerable hill farmers, forestry industries and crofters would still be paid out after Brexit.

Fergus Ewing, Scotland’s rural economy and connectivity cabinet secretary, said there was a striking contrast between Gove’s pledges to protect the £3bn in subsidies for the mainstream farming industry until 2022 and his vague stance on all other rural funding.

Scottish government officials said the Department for Environment, Food and Rural Affairs (Defra) had refused to offer long-term commitments on subsidies and grants covered by pillar two of the EU’s common agricultural policy (CAP) in a five-year programme due to last until 2020.

Those include grants worth £267m overall to Scottish foresters; the £82m Leader programme, devoted to supporting rural businesses, transport and green initiatives; £12m in funding for crofters in the country’s most isolated areas; and agri-environment schemes worth £308m.

In an interview with the Guardian, Ewing said he was particularly worried about the fate of 11,500 hill farmers in the Scottish uplands and islands, whose livelihoods and suppliers depended on subsidies worth £65.5m a year.

Ewing said he had pressed Gove to make clear and comprehensive promises that this funding would be protected during a meeting in London last month involving Defra and the devolved governments. “Unless they do [protect that funding], there will be thousands of businesses which will just stop farming. There would be whole areas of the Scottish landscape left to abandonment,” Ewing said. “What is at stake is the future of agriculture in rural Scotland.”

Fergus Ewing, Scotland’s rural economy and connectivity cabinet secretary. Photograph: Ken Jack/Corbis via Getty Images

Ewing said Gove and other leading pro-Brexit Conservatives, including the former UK environment secretaries Andrea Leadsom and Owen Paterson, as well as the environment minister George Eustace, had repeatedly promised that this funding would be protected if the UK left the EU and that the Scottish parliament’s powers over agriculture would be expanded. “The onus is on those who advocated Brexit to deliver what they promised,” Ewing said.

Defra rejected the Scottish government’s claims and insisted that Gove’s commitments extended across all CAP funding. “We know how important stability and certainty is for farmers, and that’s why we have guaranteed to match the level of farm support under both pillars of the CAP until the end of this parliament,” a spokeswoman said. “[We] will continue working with the devolved administrations, as well as farmers from across the UK, as we develop our new approach.”

Scottish officials said that statement and Gove’s previous pledges only mentioned farmers and failed to include many of the schemes they want to protect, such as the less favoured area support scheme (Lfass), crofting support forestry payments, the Leader programme and agri-environment grants.

Scotland’s hill farmers are the last in the UK to receive the special Lfass funding. Defra has promised to continue these payments only until the end of 2019 and the other funding packages under pillar two until the point of Brexit, Scottish officials say. It has not made clear whether contracts that last beyond Brexit will be honoured.

If the UK were to remain in the EU, these funding packages would last until 2020 and then be replaced by new CAP programmes. Those timescales apply to funding for farmers under the main CAP funding programme, known as pillar one.

Gove has pledged to protect subsidies for mainstream farmers until 2022, currently scheduled to be the year of the next UK general election.

Another significant sticking point is how that funding will be shared with the Scottish government, in a dispute that could have significant repercussions for Scottish budgets.

Because of the scale and remoteness of its farming and rural industries, Scotland receives 16% of all of the UK’s CAP funding. At present that money is given to Scotland separately from its Treasury grant and from the taxes raised in Scotland; that grant and tax leaves Holyrood with funding equal to about 8.9% of total UK spending – a lower proportion than it gets under CAP.

Ewing said he feared UK ministers would insist that after Brexit, agricultural funding be wrapped up in the general grant for Scotland and not ringfenced. That would mean cuts to farm and rural subsidies or cuts to other public services.