The Health Ministry said in a decree published on Wednesday patenting the drug in Brazil "was generating expectations of monopoly rights with an impact on the price of the product."
Latin America's largest country has an internationally-lauded AIDS prevention and treatment program, in which patients get free antiretroviral treatment.
The ministry said it had requested a priority examination of the patent filing by the company with the Brazilian INPI patent body, which will have to take into account the ministry's objections.
"If no patent is issued, Brazil will be free to negotiate prices of the drug, be it generic or brand name," a health ministry source told Reuters on Thursday, adding that the case was "not about compulsory licensing" or breaking patents.
A representative of Gilead Sciences Inc. in Brazil declined to comment on the issue but said high-ranking Gilead officials were in contact with the ministry to discuss the case.
The Health Ministry source said the case was different from last year's bypassing of a Merck patent for Efavirenz drug.
Last May, President Luiz Inacio Lula da Silva authorized Brazil to sidestep the patent on an AIDS drug made by Merck & Co. Inc. and import a generic version from India instead. It was the first time Brazil bypassed a patent to acquire cheaper drugs for its AIDS program.
The process then also started with the government declaring the drug "in the public interest" and saying it was too expensive to buy.
If the Tenofovir patent is rejected, Brazil may choose to import generic drug using a clause in World Trade Organization rules to flout drug patents in the name of public health.
Other countries, including Canada, Italy and Thailand, have also used the WTO clause to gain access to cheaper AIDS drugs.
(Reporting by Pedro Fonseca and Maria Pia Palermo, writing by Andrei Khalip; Editing by Derek Caney)