Devolution allows local government to control certain budgets and services in exchange for a directly-elected mayor.
The Liverpool City Region is one of 38 bids under government consideration and those behind it said discussions had actually been "very positive".
Greater Manchester was the first area to sign such a deal in November 2014.
Part of the government's northern powerhouse programme, it will eventually give the city region much greater control over transport, skills and housing.
Greater Manchester will have a directly-elected mayor from 2017.
A similar deal was signed with the Sheffield City Region earlier this month.
The six councils of the Liverpool City Region - Liverpool, Wirral, St Helens, Knowsley, Sefton and Halton - delivered their formal submission in September.
Negotiations have been led by the Mayor of Liverpool City Council, Joe Anderson, and the Leader of Wirral Council, Phil Davies who also chairs the Liverpool City Region.
Talks are still under way and, officially, the Treasury said Liverpool's bid is not falling away.
But, the minister has indicated Liverpool will not be in the first wave of successful bids.
He told the BBC the bid was "disappointing" and the document "felt more like a thesis of what they should say, rather than what they really wanted."
But Councillor Phil Davies, leader of Wirral Council and the chair of the Liverpool City Region Combined Authority, responded: "I doubt that the source of this information is actually anywhere close to the negotiations.
"In fact, since we submitted our devolution proposals on 4 September, we have had very positive discussions with the government and our stakeholders across the Liverpool City Region.
"We have prioritised our proposals, the Government has fed back that they look forward to working with us, and further meetings are imminent to maintain the momentum and negotiate on the prioritised set of proposals."
16.7  UK population (%)
16  Share of UK jobs (%)
13.3 Share of total UK GVA (%)
23   Number of universities
But one of the six council leaders, who does not wish to be named, confirmed that agreement was unlikely but said he was happy with that.
Some of the leaders are deeply sceptical about the merits of devolution, particularly the government's requirement to have a directly-elected mayor.
Some fear other councils would end up being dominated by Liverpool, but business leaders are pushing for agreement, believing it would help create jobs and prosperity.
Frank McKenna, chief executive of the business lobby group Downtown in Business, said the private sector was "concerned about the lack of ambition and the lack of focus in the initial response document".
"In fairness, the response time from government was tight so hopefully, as the negotiations continue, our submission will become much sharper.
"Crucially though, our political leaders need to sign up to the establishment of a metro mayor - this is the chancellor's price for the prize and it is one that must be accepted."
Further devolution settlements are expected by the Chancellor's Spending Review scheduled for 25 November.
A government minister has told the BBC Merseyside is not ready to get a so-called "devolution deal" following a "disappointing" bid.