The National Planning Framework sets out Holyrood's priorities for development over the next 20 to 30 years.
The last version of the document, which was issued in 2009, highlighted the importance of the Glasgow city region, with an emphasis on supporting the city centre, the Clyde waterfront and regeneration agency Clyde Gateway.
But Liz Cameron, the city council's jobs and the economy spokeswoman, said Glasgow had been sidelined in the updated version.
She said: "This is the most important national planning framework to be published for the next decade or so.
"But Scotland's biggest city has been sidelined and we do not understand why.
"The city is the powerhouse of the Scottish economy with a 11.4% share of Scotland's population and 16% of the country's jobs.
"To downplay the metropolitan area of Glasgow is inexplicable, especially given our vital economic role and the fact the city is often found to be outstanding in terms of innovative regeneration.
"We think Glasgow's contribution to Scotland should be fully recognised and I look forward to the response from the Scottish Government."
Richard Brown, the council's executive director of development and regeneration, admitted he was concerned about how the new government policy document would impact on the city.
He said: "The continued regeneration of Glasgow and the Clyde Valley, with a successful Glasgow at its heart, is closely linked with the emphasis that the Scottish Government places on its priorities for this part of the country.
"The ability to influence the shape of the city over the next 10 years depends to a great extent on how Glasgow is reflected in the National Planning Framework.
"The relative weight given to this area appears to be less than that evident in the east and north-east of Scotland.
"Given the contribution the city makes to Scotland's economy, these matters are of considerable concern to the council.
"The proposed National Policy Framework would have a significant impact on the ability of the planning authority to influence the regeneration of Glasgow and therefore to improve the city's economy."