The iPhone 6 and 6S models are similar to Shenzhen Baili's little-known 100C phone, the authority ruled.
In theory, this could lead to iPhone sales being halted in Beijing but sales continue as Apple has appealed to a higher court.
The tech giant said the handset is still available throughout China.
"iPhone 6 and iPhone 6 Plus as well as iPhone 6s, iPhone 6S Plus and iPhone SE models are all available for sale today in China. We appealed an administrative order from a regional patent tribunal in Beijing last month and as a result the order has been stayed pending review by the Beijing IP Court," the firm said.
Analyst Ben Wood, from CCS Insight, told the BBC he was confident that Apple would resolve the situation.
"Large companies will always be reluctant to settle if they feel they don't have a case to answer, but the Chinese market is so strategic to Apple that if they have to settle, they will," he told the BBC.
"This is a constant challenge for all large tech firms.
"Typically these sorts of legal spats are a game of brinkmanship."
This is likely to anger Chinese consumers who love their iPhones.
Baili is not a well-known company - they're not particularly popular.
China is Apple's second-largest market, but the patent ruling just adds to the company's problems: its iTunes Books and Movie apps were recently shut down by the authorities, and it just lost a lawsuit against a Chinese leather goods maker which stamps the name "IPHONE" on its luggage.
Earlier this month, senior US officials warned American companies felt increasingly unwelcome in China, while the European Business Council noted its members were encountering a "hostile environment" in the country.
Beijing's Intellectual Property Office has ruled against Apple in a patent dispute brought by a Chinese handset maker.