International Trade Secretary Dr Liam Fox said the aerospace giant should be "making the case" against a "no deal" Brexit in Europe - not just to the UK.
And in even stronger comments Jeremy Hunt said "threats" from businesses were "completely inappropriate".
On Friday, Airbus announced it was making plans to leave the UK in the event of a "no deal" Brexit.
Siemens (BSE: SIEMENS.BO - news) later stepped up criticism of the government by accusing it of presiding over "two years of not having achieved what we were promised, which is that this was all going to be easy".
Dr Fox told Sky News: "Companies are right to say that if there is no deal that won't be good for Britain - but it won't be good for Europe either.
:: Firms that have issued warnings over Brexit
"The point I make to them is that they should also be making the same case to European governments.
"But that will be bad for them in an era where we have got complex integrated supply chains.
"It will be necessarily bad for both sides."
:: Brexit and business - is the government listening?
Health and Social Care Secretary Mr Hunt told the BBC's Andrew Marr Show: "I just thought it was completely inappropriate for businesses to be making these kind of threats for one simple reason.
"We are in an absolutely critical moment in the Brexit discussions and what that means is we need to get behind Theresa May to deliver the best possible Brexit - a clean Brexit.
"What businesses want, and I was in business for 14 years, what they want is clarity and certainty.
"The more we undermine Theresa May, the more likely we are to end up with a fudge, which I think would be a disaster for everybody."
Mr Hunt added it was not "particularly surprising" that "multinational companies have qualms about Brexit".