According to a posting on the Web site, the veteran journalist joined Malaysiakini.com last February.
When contacted by Malaysia.CNET.com, Malaysiakini's editor-in-chief Steven Gan said Chong resigned due to personal reasons.
"His decision has nothing to do with the issue facing us," he said, referring to reports that the company had received funding from US-based financier George Soros. The online publication has denied the report, which first appeared in the Far Eastern Economic Review.
Gan added that he had no knowledge of Chong's plans for the future.
The online paper said Tuesday it will release a report next month explaining the company's seed capital from Seapa (Southeast Asian Press Alliance) as well as its revenues from other local sources.
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