Business Secretary Andrea Leadsom has told ITV News she did not speak to Thomas Cook executives as the firm hovered on the brink of collapse because it would have meant "too many cooks spoiling the broth".
Ms Leadsom had come under fire for not holding talks with the 178-year-old tour operator despite the government being aware the company was in severe financial trouble.
Talking to ITV News, Mrs Leadsom said she had left her colleague, Transport Secretary Grant Shapps, to take the lead, as the issue was considered a Department of Transport issue.
It also emerged on Monday that some Thomas Cook customers hit by the collapse may have to wait as long as two months to receive a refund, according to the Civil Aviation Authority (CAA).
Direct debit customers will be refunded within 14 days, but others will have to wait up to 60 days, with 360,000 customers awaiting payment, the CAA said.
But, Ms Leadsom, said she had spoken frequently to Mr Shapps.
"I picked up the phone to Grant Shapps, who picked up the phone to Thomas Cook.
"So the point is you don't want to have mixed messages, or too many cooks spoiling the broth," she told ITV News.
"It was really important that we were very clear.
"This was an enormous collapse.
"What we couldn't have was one secretary of state saying 'is it going to collapse, and what time is it going to collapse?'.
"You could not possibly afford to have mixed messages.
"So it's absolutely right that one secretary of state takes lead, and in the case of Thomas Cook that was the Department of Transport."
Following Thomas Cook's collapse, Ms Leadsom launched a taskforce which will consider support available for employees looking for new opportunities, for apprentices looking to continue their training, for employees returning from abroad, and for individuals and families needing access to benefits.
It will also review recovery for local communities including Peterborough, where the firm has its retail headquarters, and Greater Manchester, where many employees were based, exploring backing for local businesses and high streets through discussions with local growth hubs and authorities.
Ms Leadsom's comments came as Thomas Cook staff demanded financial support from the government following the collapse of the travel giant, with dozens of former employees - some wearing their old uniforms - protesting outside the Conservative Party Conference.
They urged ministers to "pay us now" after they did not receive their wages on Monday.
Around 9,000 staff in the UK were left jobless last week when the business failed to secure a last-ditch rescue deal.
Mayor of Greater Manchester Andy Burnham led calls outside the Tory conference venue in the city for the government to give former staff their unpaid wages and redundancy packages.
Asked what the government needed to do to help the workers, he said: "Get payments made without any delay - so that's both unpaid wages and redundancy, which is obviously a statutory service.
"I think they need to help us with regard to retraining if people want to retrain, but I think they also need to provide better answers - why did the German authorities save their airline, and why was the profitable UK airline allowed just to go to the wall?"
Shadow business secretary Rebecca Long Bailey and Labour's Lucy Powell, who represents Manchester Central, addressed the crowds along with Mr Burnham.
Ms Long Bailey said: "Over the weekend it surfaced that the Beis (Business, Energy and Industrial Strategy) department didn't meet with Thomas Cook hardly at all over the last 12 months and we wonder why that was allowed to happen when it was quite clear that there were alarm bells ringing about Thomas Cook for quite some time.
"It's staggering how the German government seemed to be on top of the situation and intervened, yet ours just sat back and sat on its hands essentially. And there must be reasons for that.
"We want to know, is it incompetence or was there a real strategic reason as to why they didn't want to provide the support?"
Mr Shapps has previously defended the Government’s decision not to bail out the failing company, saying it risked throwing “good money away after bad”.
“I have seen it suggested in the papers that the Government should have avoided the collapse with a bailout of up to £250 million," the Transport Secretary said.
“Given the perilous state of the business, including the company’s own reported £1.5 billion half-year loss reported in May followed by a further profit warning in November, this was simply not the case, with no guarantee that an injection would have secured the future of the company.
“Our concern was we would put £250 million at risk and thrown away good money after bad then still have to pay the cost of this repatriation.”