Sajid Javid has announced £472m will be handed to the Scottish Government over the next two years.
As agriculture is a devolved matter, it will be down to Holyrood ministers to oversee the allocation to farmers.
It comes as the UK prepares to leave the Common Agricultural Policy (CAP) direct payments scheme, which supports farmers across Europe with subsidies in 2020. This will be replaced by a new system based on public money for public goods.
The cash injection will allow the funding for direct payments for 2020 to continue at the same level as this year and supplement the remaining EU funding that farmers will receive for development projects until 2023 at the latest. The UK Government has pledged to guarantee the existing annual budget to farmers in every year of the Parliament.
The announcement is on top of the £216m in funding awarded since the spending round to support the farming sector in Scotland and Wales.
The Scottish Government has previously warned Brexit was “by far the biggest threat” to farming north of the Border.
Mr Javid said: “When we leave the EU and are freed from the Common Agricultural Policy, we will be able to support our vital rural communities – who are a cornerstone of life in the UK – with a fairer and less bureaucratic system.
“Farmers can enter the new year with confidence that they have our backing and will be able to thrive after Brexit.” Moray MP Douglas Ross, a Scotland Office minister, said: “Farming is vital to Scotland’s economy and we will always back our farmers.
“The £472m UK Government support for Scottish farmers for 2020 is on top of the recently announced boost of over £211m – £160m of which will resolve the issue of historic convergence allocations.
“For too long our farmers have been given a poor deal by the Common Agricultural Policy and we will make sure they have a prosperous future outside of the EU.
“When we get Brexit done, we will tailor support better to Scotland’s unique farming environments.”
Environment secretary Theresa Villiers said: “Outside the EU we will have a simpler, fairer funding system
A spokesman for Holyrood rural economy secretary Fergus Ewing: said: “This announcement does not provide the level of certainty or reassurance that our farmers need to plan for their future. As the National Farmers Union has pointed out, this is not new money and only maintains current levels of support. It also appears to be for one year only rather than provide the traditional certainty over five years.
“Our rural economy is on the front line of the potential impacts of Brexit, with remote and rural areas likely to be hit the hardest if we have to leave the EU and lose tariff and barrier-free access to trade.
“The Scottish Government has already long campaigned for the UK Government to rectify a ‘historic wrong’ in failing to pass on Scotland’s rightful share of convergence funding between 2014 and 2020 and it is only now that we have been able to start passing this on to our farmers and crofters, providing some support and security during these uncertain times, and enabling them to invest in their businesses, pay down debt and ultimately drive the rural economy forward.”