Ministers are trying to reform the current system, which last year paid one farmer more than £3 million of public money. They want to find a way to pay "active" farmers more while closing the loopholes that allow so-called "slipper farmers" to be paid large sums for doing nothing.
But land reform campaigner Andy Wightman has said that under the current plans, ministers risk simply rewarding the largest landowners while smaller farms and crofters lose out.
He has calculated that the Duke of Westminster, who owns 37,303 hectares of eligible land in Sutherland, could qualify for £764,712 for each of the next six years, although he made no claim last year.
The Duke of Roxburgh received £204,374 in 2013 and his 4637 hectares in the Borders could attract support of £950,585 per year under the new rules.
Meanwhile, Smech Properties Ltd, a company belonging to Sheikh Mohammed bin Rashid Al Maktoum, the King of Dubai and Prime Minister of the United Arab Emirates, owns an estate in south west Ross-shire that received £26,406 in 2013 but could be eligible for £439,192 a year until 2020, according to Mr Wightman.
Even the Queen, who does not claim, could receive more than half a million pounds for the 25,000 hectares of Balmoral Estate.
Mr Wightman is also concerned that, instead of the new system being introduced in 2015, it will be phased in over the next six years.
He said that would mean Frank Smart, who farms near Banchory and received £3.22m last year under the existing system, would continue to receive a large proportion of his payments until 2020.
The existing system of farm subsidies, awarded under the European Common Agricultural Policy (CAP), is coming to an end in December 2015 and the Scottish Government is currently finalising the details of the new scheme that will run until 2020.
Currently, Single Farm Payments are awarded to farmers on the basis of what they received in 2000-2002, with the amounts paid based on their farming activity at that time.
Mr Wightman said: "Some farmers 'gamed' the system by increasing their farming activity in those years, and thus have done very well out of it over the past decade."
From next year, a new Basic Payments System of farming subsidies will be introduced. It will be a fixed payment per hectare of land farmed, with one rate of €20-€25 (£16-£21) for rough grazing and €200-€250 (£165-£205) for better-quality land.
A Scottish Government spokeswoman said that unlike in the last 10 years, farmers would have to demonstrate they meet minimum activity levels, to help clamp down on "slipper" farming.
She said: "Scotland needs a CAP that supports dirty wellies and not comfy slippers, and we need to ensure only active farmers are supported under the new CAP. As Scottish farmers will have the lowest payments rates in Europe, it is even more essential that this support is directed towards genuine farmers."
But Patrick Krause, chief executive of the Scottish Crofting Federation, said there was a great deal of uncertainty. "The fact they are talking about paying so much less to those on rough grazing less is very worrying for crofters," he said.
The landowners organisation Scottish Land & Estates also has concerns, although Andrew Midgley, its head of policy, said members did not want to see the emergence of a new 'slipper farmer' issue. "The further we get from the 2000-2002 historic reference period, the more unsustainable and iniquitous the system has become," he said.
However, he added it should not be assumed there would be a bonanza for landowners and that area payments represented a positive step forward.
Mr Smart could not be contacted for comment.