Writing a big cheque for agriculture is going to be harder for the British government post-Brexit, one of Theresa May's key advisors has said as he raised the prospect of a change in the way subsidies are allocated.

George Freeman, who is chairing the Number 10 policy board, said the agriculture sector was likely to see the most profound 'shake out' of Brexit.

Speaking on the fringes of the Conservative Party conference, the Mid-Norfolk MP said: 'I would have thought knowing parliament that if the British electorate looked at a chunk of money that was going to British agriculture, the likelihood of them saying I would rather more of it went to the NHS is quite high.'

It comes after environment secretary Andrea Leadsom said that it was crucial farmers were provided with certainty and continuity, using her first party conference speech to say it was 'really important' that the government had confirmed the same level of agricultural support until 2020.

Mr Freeman, the former life sciences minister, who was given the new role in Theresa May's summer reshuffle, said that he thought it was likely the level of subsidy was going to change.

'We are going end up supporting those bits of farming that clearly wouldn't work without some support. I just think the British electorate will say hang on a minute, we understand why marginal hill farmers, why people who couldn't exist without support need some help...but I think they may have a bigger problem with 'you mean we are writing a big cheque every year' that we used to turn a blind eye to when it was Europe, but if it has got HMG [Her Majesty's Government] on it is going to be harder.

'That will require us to explain why that industry, which is a key strategic industry to competitiveness, trade, agri-tech, needs a different form of support. I think will probably see a variation.'

It comes after shadow foreign minister Emily Thornberry, who is spearheading Labour's Brexit strategy, said there was currently a 'serious problem' with the current arrangements, which she claimed saw wealthy landowners who do no require subsidies receiving the biggest payments, while farmers on the lowest incomes received no extra support.

In her early blueprint of Labour's priorities in the negotiations to leave the European Union, she said that leaving the Common Agriculture Policy would require a 'wholesale rethink of agricultural policy in the UK'.

She indicated that as a minimum, Labour would demand that any replacement system of direct payments was reformed so it did not just relate to the size of farms, but also to factors such as the location and type of farm, its productivity and profitability.