The study, by planning consultancy Nathaniel Lichfield & Partners (NLP), said the Greater Manchester Spatial Framework (GMSF) could push up house prices and deter vital skilled workers from moving to the area.
Chancellor George Osborne said two years ago that northern cities would be given new powers, infrastructure and cash to help rebalance the national economy.
But the NLP study said the draft GMSF – which is aimed at managing the use of land in the region to 2035 – aimed for an average of just over 10,000 homes to be built each year.
"As it currently stands, we believe that there is a clear strategic disconnect between the Northern Powerhouse growth ambition and the suppressed housing and economic analysis at the heart of the emerging GMSF," the report warned.
"If Greater Manchester is to underpin the Northern Powerhouse, driving growth and reducing national inequalities as envisaged by the government, the GMSF must be more proactive in supporting economic growth and provide a clear vision for boosting housing provision to service a new, highly skilled, workforce."
The report said that unaffordable and poor quality housing could act as a disincentive to companies looking to invest in an area.
"The GMSF, as currently drafted, will result in a situation whereby companies will struggle to recruit and retain talented graduates and more senior employees, negatively impacting on the overall attractiveness of the region and potentially resulting in investment going elsewhere," it warned.
A Greater Manchester Combined Authority spokesman said: "The Greater Manchester Spatial Framework (GMSF) will outline how many new homes we need and how much land is required for new businesses and employment but it also means looking at how we can do this in a way that creates attractive places that people want to live and work in.
"Greater Manchester Leaders are currently considering consultation responses to GMSF growth options, one of which is based on targets promoted by the Housing the Powerhouse group. A detailed draft Spatial Framework will be released towards the end of the year. This will set out our targets and how we plan to grow Greater Manchester.
"To meet the ambitious growth targets of the Northern Powerhouse, Greater Manchester will need to deliver at least a quarter of it. This means beating business-as-usual growth in GM by some £14bn per year in real terms by the early 2030s; equivalent to an extra 27% of GM's current economy on top of business-as-usual. Greater Manchester Leaders are committed to making this ambition a reality."