Transport chiefs have vowed to continue their fight for more Government funding despite the "setback" of having a £1.7 million bid turned down.
The Leeds City Region Partnership, which consists of 11 Yorkshire authorities including Bradford Council, would have used the money to fund research into congestion.
The bid has been knocked back, prompting business and council leaders to hit out at the Government.
Councillor Stanley King, chairman of Metro, said: "If the Government wants us to engage in regional activities, it will require a lot of detailed research.
"Funding for this has to come from Government because existing budgets are already tied up.
"On the one hand, the Government wants us to think on a regional basis, but on the other they are not giving us the tools to do it."
Councillor Chris Greaves, Bradford's representative on Metro, said authorities could look to make use of existing data as an alternative to major studies.
He said information gathered by the authorities for different reasons, including road safety surveys, should be fed into a central bank of knowledge to build up more data "by default."
Coun Greaves added the Government only seemed interested in bids which outlined proposals for road pricing, a strategy that does not form a part of current thinking in the region.
Leeds City Council leader Councillor Mark Harris said: "This Government has again chosen to ignore the prosperity, health, environment and social inclusion of people across the Leeds City Region.
"It wanted an up-front commitment to road pricing, which we made clear we were not prepared to give without proper analysis and commitment from the Government to the public transport schemes that would give people an alternative to using their cars."
The Forum of Private Business (FPB) has urged Transport Secretary Douglas Alexander to take a broad approach to tackling congestion.
Nick Goulding, chief executive of the FPB, said: "The system must look at moving traffic from busy routes to viable alternatives. That means improving public transport and moving more freight onto the railways."
The blow comes less than a week after the Leeds City Region Partnership unveiled a vision containing even greater requests for central Government funding.
e-mail: will.kilner@bradford.newsquest.co.uk
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