The commission’s decision, published yesterday, says the regulator found that although some of the pro-hunting organisation’s purposes were exclusively charitable for the public benefit, not all were, so it could not be registered as a charity.
The alliance said its legal advisers "interpreted the law very differently" from the regulator and it was considering an appeal.
The regulator found that the primary result of the promotion of agriculture, game and food production, one of the alliance’s proposed purposes, would be commercial benefit to those involved in such activities.
"The private benefit flowing from this activity appears therefore to be more than incidental to the public benefit flowing from it," the regulator’s decision says.
"It also seems difficult to draw a direct analogy with the promotion of agriculture for the public benefit, which has a focus on the improvement of the industry generally, rather than the promotion of specific products of the industry."
The commission also concluded that certain purposes relating to practices including hunting, shooting and fishing were not considered charitable in law.
"Some of the alliance’s purposes are charitable, and the commission recognises that the alliance does important work protecting and promoting rural life and representing the interests of people living and working in the countryside from all backgrounds and geographical locations," the regulator said in a statement alongside the decision.
"But not every purpose that is beneficial to society is a charitable purpose for the public benefit."
Members of the alliance voted in 2014 for the organisation to apply to become a charity in its own right.
The alliance already has a charitable arm, the Countryside Alliance Foundation, which was registered by the commission in 2007. It provides activities including falconry for schools and a programme that combines fly fishing and support for women with breast cancer.
Tim Bonner, chief executive of the Countryside Alliance, said that if the regulator’s interpretation of the law was correct it exposed a "fundamental problem with charity legislation".
He said: "The Countryside Alliance is disappointed that, although the Charity Commission recognises the important work we do protecting and promoting rural life and representing the interests of people living and working in the countryside from all backgrounds, it does not believe that it is possible to bring such work within the legal definition of a charity.
"It cannot be right that the law discriminates against activities that clearly should be charitable and which the Charity Commission itself recognises as important work that is beneficial to society, while bestowing the advantages of charitable status on activities that have far less public benefit. We will consider an appeal in order to clarify the law."