Eligible Welsh farmers currently receive annual payments through the European Union’s Basic Payment Scheme.
On Tuesday, Rural Affairs Secretary Lesley Griffiths said payments would continue as usual in 2018 and 2019.
However between 2020 and 2025 a “gradual, multi-tier transition” will take place towards a new system.
Farmers in England have been guaranteed payments at the current EU level until the 2022 general election.
Ms Griffiths said: “Brexit brings significant changes and we must have a well-planned and multi-year transition.
“I have always been clear that we should not lose a penny of funding as a result of leaving the EU and I will continue to fight to protect a full and fair allocation of funding to support land management in Wales.
“From 2020 powers will return from Europe. I then envisage a gradual and multi-year transition from existing to new schemes.”
Ms Griffiths also said farmers may need to do things differently to receive funding in the future.
“This is the only way we can ensure our land delivers greater benefits,” she said.
“We need a prosperous and resilient agricultural sector in Wales, whatever the nature of Brexit.
“To make this a reality, we need to change the way we support farmers.
“We intend, therefore, to have two elements of support, one for economic activities and one for public goods production.”
Responding to the announcement FUW President Glyn Roberts said: “We welcome the assurance given regarding the 2019 scheme year, but whether a five year transition period from 2020 is appropriate will depend upon a whole set of circumstances which are as yet unknown.
“These include the nature of any post-Brexit deal with the EU and what exactly we are transitioning to.”
NFU Cymru President John Davies said: “We are pleased to hear that the cabinet secretary recognises the need for a sufficiently long transition period which will take us through to 2025.
“This is crucial not just for farming businesses but for the rural economy that relies on thriving farming businesses and for our food processing sector who need guaranteed supply to ensure that their plants can run efficiently.”
He added: “The decisions that we face should not be taken lightly or on a whim and the impacts must be considered carefully and we would ask that the Welsh Government must ensure that it carries out a full economic impact assessment of each and every proposal under consideration.”
The cabinet secretary has told AMs further details will be set out in July and a consultation process will follow.