Macfarlane was attending a post-match media conference with NBA stars James Harden and Russell Westbrook in Tokyo Thursday, but neither men were allowed to answer her question on whether they would feel comfortable speaking out on political and social issues in the future.
The league is currently facing a backlash from China after Rockets' general manager Daryl Morey tweeted his support for the pro-democracy demonstrations in Hong Kong.
He has since deleted the post but all of the NBA's official Chinese partners have now suspended ties with the league as it continues to grapple with the fallout.
Harden, in particular, seemed happy to answer the question but was prevented from doing so by the media officer off-screen, despite Macfarlane's follow-up question.
NBA spokesperson Mike Bass later apologized for the incident, saying: "During today's Houston Rockets media availability, a team representative inappropriately interjected to prevent CNN's Christina Macfarlane from receiving an answer to her question.
"We've apologized to Ms. Macfarlane as this was inconsistent with how the NBA conducts media events."
Earlier in the press conference, Macfarlane was able to ask Rockets' coach Mike D'Antoni if he had a message for Chinese fans who might have felt let down by the NBA over the spat.
"It's a tough situation, very difficult. Adam Silver speaks for the NBA, I work for the NBA, I go with Adam. Commissioner Silver will do the right thing," he said.
Tim Frank, an NBA senior vice-president, later called Macfarlane to personally apologize for what happened when she attempted to ask her question to Harden and Westbrook.
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