A report by the Centre for Cities thinktank has identified the scale of the "jobs deficit" facing the region with 69,500 posts required just to raise levels to the national average.
It reveals that even before the recession hit, many areas were struggling, with Barnsley, Bradford, Doncaster, Hull and Huddersfield losing private sector jobs. Now the likes of Hull and Sheffield face a combined deficit of nearly 40,000 posts.
Although Wakefield and York have successfully attracted new business and achieved employment rates higher than the national average, the Centre for Cities warns of tough challenges ahead for the new Coalition government.
It states that as the public sector faces savage cuts, Westminster must support the expansion of cities where businesses are already adding private sector jobs.
The director of policy at the Yorkshire and Humber Chambers of Commerce, Nick Pontone, said: "The finding that the boom years seemed to bypass a number of Yorkshire cities is obviously a major concern.
"Every city has a different story so these sorts of comparisons are often unfair.
"However, the bottom line is that a number of our region's cities know they have a longstanding problem with employment. They must be supported to kickstart private sector growth, not abandoned as the report implies."
The statistics revealed that Sheffield and Hull have the biggest jobs gap to make up, with a deficit of nearly 20,000 each, although Mr Pontone said the figure could be misleading as in Hull there was a reasonably high proportion of private sector jobs and therefore less exposure to public sector cuts.
The chief executive at Leeds, York and North Yorkshire Chamber of Commerce, Gary Williamson, said he was pleased that York had successfully brought in business while the Leeds deficit was a relatively low 9,000.
He said: "It is great that the report recognises the importance of private businesses as employers and wealth creators in our area.
"For this to continue, the new government must deliver the confidence and the environment that our businesses need and avoid stifling enterprise through red tape, the employer's National Insurance increase or a lack of infrastructure."
The report states that the Labour Government tried to redress the jobs deficit – which nationally stands at more than 600,000 – by adding large numbers of public sector jobs to struggling city economies and creating regional development agencies to support private sector growth.
However it finds that some areas in the north which grew as ports, dockyards and factory towns now find themselves isolated from international airports, universities and motorway transport links that businesses rely on to grow.
Deputy Prime Minister and Sheffield Hallam MP Nick Clegg said he is determined to avoid the mistakes of the 1980s which created "a North-South divide".
He said: "We'll take good measures so these cities in the North, our great Northern cities, are given the support they need.
"David Cameron was in Leeds last week and announced there will be senior members of Government allocated to all our great cities so each will have a voice at the top of Government.
"I think with these kind of measures we can balance the books and create jobs and low interest rates."
The report comes as the Institute for Public Policy Research North called on the northern regions to "carve out their own futures, define their own regional economic identities and transform their public services".
Director Ed Cox said: "This is a time for leading not pleading. "What is needed is leadership, collaboration and clear vision as well as a healthy dose of compromise and pragmatism."