The Environment Secretary warned border checks would add to costs for food producers.
Michael Gove told the Oxford Farming Conference that leaving the EU without a deal would put at risk "real gains" from Brexit' like a productivity boost or protecting the environment.
He also warned of the impact to sectors such as agriculture if the UK crashed out of the European Union.
While he said a nation as adaptable, resilient and creative as the UK would flourish over time even without a deal, "the turbulence which will be generated by our departure without a deal would be considerable".
Mr Gove added: "It would hit worst those who are our smaller farmers and farm businesses."
He said tariffs, border checks and labour pressures would all add to costs for food producers.
"Nobody can be blithe or blase about the real impacts on food producers in this country of leaving without the deal," he told the conference.
While Mr Gove flagged up the challenges that would face farmers and the food industry exporting their products, he played down the risk of consumers facing shortages on supermarket shelves.
"We are doing everything possible to ensure that when it comes imports both of food and veterinary medicines that we can maintain continuity as effectively as possible," he said.
"We've taken steps to ensure a continuity approach. There shouldn't be a problem with food coming into the country."
He said leaving the EU would rejuvenate the UK's democracy, make power more accountable and allow the UK to escape from the "bureaucratic straitjacket" of Europe's Common Agricultural Policy, which currently controls farm regulation and the subsidy system.
And it will "develop a more vibrant farming sector with access to technologies on which the EU is turning its back".
Mr Gove has previously set out plans for payments for "public goods" such as managing land for flood prevention, creating habitats for wildlife, delivering clean water and improving public access to the countryside.
In his speech he said: "Leaving the EU will end support for inefficient area-based payments, which reward the wealthy and hold back innovation.
"And we can move to support genuine productivity enhancement and public goods like clean air, climate change mitigation or the improvement of soil, or water quality or improvements to pollinator
"All of these are real gains that our departure from the EU can bring, but these real gains risk being undermined if we leave the EU without a deal," he warned, urging Parliament to support the Prime Minister's deal.
Quizzed on whether the £3.2 billion the UK's farmers receive in funding through the EU's subsidy scheme was under threat, Mr Gove insisted it was not.
He said the money was guaranteed until the end of this Parliament, and that the case needed to be made for more investment, if farmers embraced reform in the sector and the value of public goods could be demonstrated.
Looking beyond Brexit, Mr Gove said the world is facing a fourth agricultural revolution, with new technology from gene editing to artificial intelligence, robotics and data analytics to reduce costs and improve yields.
"If we embrace the potential of the fourth agricultural revolution we can guarantee the future of the UK as a major global food producer."
He also said farmers embracing change and reform would help unlock support from the Treasury, which wants to back growth and innovation.
National Farmers' Union president Minette Batters said that, less than 90 days away from Brexit, there was still "enormous uncertainty" about the future and how domestic food production would fare.
The NFU warns that British agriculture could face huge disruption as a result of not being able to export agricultural products to the EU if its role as an exporter has not been re-approved by Brussels by March 29.
The lamb industry could be particularly hit as 31% of its produce was exported in 2017.
In a no-deal scenario, exports to the EU from the UK could face huge tariffs, with beef potentially seeing a 65% duty, and lamb suffering 46%, which could push up the costs for businesses.
Imports could also be affected, with severe delays at ports of essential items such as veterinary medicines, fertilisers, feed and machinery parts.
And there is a risk of opening the UK to goods that are not produced to the high standards of food safety, animal welfare and environmental protection British farmers meet, the NFU said.
Mrs Batters said: "There have been enough warm words and comfort to us as farmers, but now is time for decisions from the Government about how it will secure the nation's food supply."