Maya Wang, a senior China researcher with Human Rights Watch, said there could be legitimate concerns of misuse of apps but that the statement from Apple was "disingenuous" because it did not make any reference to pressure from Beijing in the People's Daily commentary.
The company's decision angered Apple users in Hong Kong - even those who have not been protesting in the streets.
Apple caved in to Beijing's edict and permanently removed a controversial app from its App Store on Thursday, days after Chinese state media, already in the hunt for Western businesses aiding and abetting Hong Kong protesters, pounced on HKmap.live as it helped demonstrators evade arrest.
"Criminals have used it to victimize residents in areas where they know there is no law enforcement", Apple said. It also reportedly removed the Quartz app in China over the site's coverage of the Hong Kong protests. But Apple quickly reversed its decision, approving the app for sale in Hong Kong.
Hong Kong has been rocked by four months of increasingly violent protests, initially against a now-shelved extradition law, but whose focus has now shifted to broader pro-democracy aims.
The iPhone manufacturer had the fifth biggest market share in the country in the second quarter at 6.7 percent, well behind leader Huawei and other domestic companies, according to data from the Chinese-owned International Data Corporation.
The tech giants are the latest US -based companies to get enmeshed in ongoing anti-government protests in the lucrative territory.
However, the app's makers say there's no evidence their app has been used by people to ambush police in the city.
In a Wednesday statement, Apple said that it had heard concerns about the app from many Hong Kong customers. Both rapidly backtracked. Pro-democracy protesters have called for a boycott of Maxims, the catering giant that operates the Starbucks and Yoshinoya restaurant franchises in Hong Kong, after Annie Wu Suk-ching, the daughter of its founder, labeled protesters as "rioters" at a United Nations conference. "This sounds rather disingenuous", she said.
The app's developer insists that HKmap.live is created to help everyone stay safe and isn't specifically designed for protestors.
But the chief executive has been criticised for "taking at face value" the claims of the Hong Kong police, which don't chime with the experiences of global observers on the ground.
Neither China's foreign ministry nor the information office of the State Council had an immediate comment when asked about the HKmap.live app removal.
Charles Mok, a member of Hong Kong's legislative council, wrote to Cook saying he was "deeply disappointed with Apple's decision to ban the app, and would like to contest the claims made by Hong Kong police force".
But Hong Kong's protests have been fuelled by resentment of what many residents see as relentless efforts by Beijing to exert control over their city, despite the promises of autonomy. It also still works on some non-Apple devices.