In an op-ed published late Tuesday in China Daily, the state-backed newspaper shot down Silver's response, saying it shows the league's initial response that it respects China and its history was "nothing but an attempt to prevent the hemorrhaging of profits made in China."
The remarks highlight the escalating tensions between the NBA and China over a tweet sent out by Houston Rockets general manager Darly Morey in support of the anti-government protests in Hong Kong, which was deleted very quickly.
Despite Morey sending tweets to diffuse the situation, the comments sparked anger in China, leading to broadcasters pull pre-season games from their networks, e-commerce sites de-listing Rockets merchandise, and brands re-assessing their relationship with the NBA and the Houston franchise.
The NBA initially put out a statement saying that it had "great respect for the history and culture of China." Then Silver addressed the incident more directly, in apparent support of Morey's right to free speech.
"It is inevitable that people around the world — including from America and China — will have different viewpoints over different issues. It is not the role of the NBA to adjudicate those differences," the NBA commissioner said.
China Daily said the change from what it dubbed a "honey-mouthed statement" by Silver "shows his organization is willing to be another handy tool for US interference in the special administrative region."
"If Silver thinks endorsing the indiscriminate violence the radical Hong Kong protesters are resorting to in their bid to 'liberate' the city, a secessionist pipe dream they are peddling to justify their summer hooliganism, is supporting freedom of expression then he should think again," the newspaper wrote.
"The violent spectacles staged by radicals in Hong Kong are intended to sensationalize and amplify their voices at the expense of the many in Hong Kong who do not support their actions."
Hong Kong is a semi-autonomous city which operates under the "one country, two systems" principle, granting its citizens a certain degree of financial and legal independence from the mainland.
Anti-government protests have rocked the city for four months now. They first erupted over a now withdrawn extradition bill that would have allowed fugitives to be transferred to mainland China for trial.
The NBA's China crisis has also drawn comments from American politicians who initially accused the league of bowing to Beijing's pressure and putting money over human rights.
Another state-backed publication, the Global Times, said Silver will "offend more people no matter what he tries to say."
"Neither Chinese public opinion nor U.S. public opinion is satisfied with his comments. The crazier the political correctness in the US is, the stronger the backlash on the Chinese internet," the Global Times wrote. "The result is that the U.S.' arrogance is killing the NBA market in China."
The editorial claimed that the NBA's market in China is "faces unprecedented challenges."
The NBA was not immediately available for comment on either editorial when contacted by CNBC.
— CNBC's Grace Shao contributed to this report