The confidential assessment, published in a Sunday newspaper, said the Swedish-produced model "never reaches the Meet Minimum Expected Capabilities in all type of missions."
Maurer's spokeswoman told DRS radio that the minister "had no knowledge of the contents of the report."
She said the defence ministry would now establish "how much weight to give the report in the evaluation process."
The selection of Saab's Gripen over French planemaker Dassault's Rafale and the Eurofighter, produced by the EADS consortium, has been the subject of much press scrutiny.
In announcing the decision in November, the Federal Council said the deal -- 22 planes for an estimated 3.1 billion francs ($3.4 billion) -- met airforce needs without compromising the budgets of other military branches.
Extracts of the 2009 report by the Swiss air force, published by Le Matin Dimanche, said tests carried out the previous year had shown "the overall effectiveness of the Gripen MS21 remains inadequate to achieve air supremacy in the face of future threats beyond 2015."
The Swiss government must formally endorse the Gripen deal this month and it will then be sent to lawmakers for final approval later this year.
Dassault has reportedly made a counter-offer undercutting the current deal, prompting Saab to review its price.