Some analysts wonder whether Xi or the central government supported the actions of Guangdong officials.
Some blame the row squarely on Tuo Zhen, the newly appointed provincial propaganda chief. One observer in Guangdong blamed his "behavior and work style" for causing the row.
But others see the controversy as bigger than just the Guangdong Propaganda Department versus the Southern Weekly.
"It is a publicity crisis for Xi Jinping's new administration," said Xiao Qiang, a founder and editor-in-chief of China Digital Times, a U.S.-based site monitoring China's Internet and media issues. "Its political credibility and ability to lead is now being tested.
"When the top leadership seems not resolute and clear, a smaller event moves into the national public sphere, and the state even just slightly loses control of the message in the media and Internet space."
For the Global Times, however, the message is clear.
"No matter how the Chinese media is regulated, they will never become the same as their Western counterparts," the government-backed media group said in an editorial. "This should be the basic judgment of Chinese media professionals.
"China's political system differs from the West's, and the media cannot separate itself from a country's political reality. The only way that fits the development of Chinese media is one that can suit the country's development path."
According to the China Digital Times, the Central Propaganda Department has issued an urgent directive telling media groups at all levels that:
-- State-run media is an unswerving basic principle
-- The "mishap" at Southern Weekly has nothing to do with Guangdong propaganda chief Tuo Zhen
-- The incident's development is due to the "meddling by hostile forces"
The directive told all editors, reporters and staff to discontinue voicing their support for the Southern Weekly and ordered all media sites to prominently republish the Global Times editorial.