Businesses have warned that food prices may rise and jobs may be affected after the chancellor vowed to end alignment with EU rules after Brexit.
Sajid Javid told the Financial Times the UK would not be a "ruletaker" after Brexit, urging businesses to "adjust".
The Food and Drink Federation said the proposals were likely to cause food prices to rise at the end of this year.
The Confederation of British Industry said for many firms, keeping existing EU rules would support jobs.
The automotive, food and drink and pharmaceutical industries all warned the government last year that moving away from key EU rules would be damaging.
'Death knell'
In an interview with Financial Times, the chancellor said the Treasury would not support manufacturers that favour staying aligned with EU rules, as companies had known since 2016 that the UK was going to leave the EU.
"Admittedly they didn't know the exact terms," he said.
The UK's 11-month transition period begins after it leaves the EU on 31 January.
Mr Javid declined to specify which EU rules he wanted to drop, but said some businesses would benefit from Brexit, while others would not.
He added: "There will not be alignment, we will not be a ruletaker, we will not be in the single market and we will not be in the customs union - and we will do this by the end of the year."
Tim Rycroft, chief operating officer of the Food and Drink Federation, told BBC Radio 4's Today programme that it sounded like the "death knell" for frictionless trade with the EU.
Acknowledging that some industries might benefit from Brexit, he said: "We also have to make sure the government clearly understands what the consequences will be for industries like ours if they go ahead and change our trading terms."
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