Sammy Wilson has been accused of being "out of step" with business groups after the DUP MP claimed a number of firms' representative bodies were scared to speak out about the Windsor Framework.
The East Antrim representative said business organisations needed to "stop being so cowardly and afraid of being accused of being political".
The ardent Brexiteer made the comments in the News Letter following the news that up to 500 jobs could be lost with the closure of Co Armagh refrigerated transport company Morgan McLernon.
In a letter to employees announcing that the firm was closing its facility in Lurgan, the company's chief executive John Kerrigan said the business had been in an "unsustainable financial position" for some time and that matters were "not helped by Brexit and many other external factors".
There was no mention of February's revised protocol deal between the UK and EU, which has yet to be fully implemented.
In March, days after the Windsor Framework was agreed, Mr Kerrigan said: "It has been a difficult few years in the Northern Irish logistics market post-Brexit, not to mention the many challenges that the whole of the UK has faced since, and continues to face."
The company has declined to comment further.
The Windsor Framework received a cautious welcome from the NI Business Brexit Working Group, an umbrella body representing 14 industry groups.
Manufacturing NI: Windsor Framework 'a unique economic opportunity which must be grasped'
Mr Wilson said Morgan McLernon was a closing its operation in Northern Ireland "because of the difficulties caused by the devastating and damaging deals" the British government made with the EU.
He said the agreements had been "negotiated by successive spineless and supine prime ministers" and that business organisations had failed to speak out about the implications.
The DUP's Westminster chief whip said those affected by the Windsor Framework needed to "complain loudly".
"Business organisations must find their voice and stop being so cowardly and afraid of being accused of being political," he said.
"This is a political issue but it affects their members."
Mr Wilson advocates an alternative arrangement in which the EU and the UK "mutually enforce each others laws and regulations when it comes to trade across the border".
"Such an arrangement would ensure that NI is not split from the rest of the UK constitutionally and economically and the EU single market is not damaged by unsupervised trade coming into it from NI," he said.
But Alliance deputy leader Stephen Farry said business organisations were "more than capable of making their own independent judgements on what is best for their members and the wider economy".
He said the Windsor Framework was an improvement on the protocol.
"While it continues to pose issues for certain sectors, overall it offers Northern Ireland some competitive advantages which businesses are keen to exploit," the North Down MP said.
"Perhaps the real question the DUP should be reflecting upon is why they are so out of step with not just most business voices but stakeholders across society."
SDLP MLA Matthew O'Toole said Mr Wilson's remarks were "another example of his complete lack of self-awareness or interest in the needs of the local economy".
"The overwhelming preference of the business community is that a devolved government is needed urgently to provide political stability to enable them to make basic investment and recruitment decisions," he said.
"The Windsor Framework represents meaningful progress and presents real economic opportunity for this region via dual market access."
The South Belfast representative said Mr Wilson's language would fuel a growing perception that the DUP is "hopelessly divided and cannot provide the leadership the businesses and workers of this place deserve".
