The Media Development Authority (MDA) said it has ordered Yang Kaiheng, 26, and Japanese-Australian Ai Takagi, 22, to take down the The Real Singapore (TRS) website as well as its associated online and social media accounts by 1200 GMT.
The media regulator said in a statement it had suspended the pair's "statutory class licence" to operate the website, which in general is automatically granted without a need for application to people who operate websites inside and from Singapore.
The website went offline on Sunday evening, while its widely followed Facebook and Twitter accounts were also shut down.
"The Real Singapore has been ordered to disable access to all our online services by the Media Development Authority (MDA) of Singapore," read a message on the website.
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The MDA said the website "has deliberately fabricated articles and falsely attributed them to innocent parties".
"TRS has also inserted falsehoods in articles that were either plagiarised from local news sources or sent in by contributors so as to make the articles more inflammatory," the statement said.
The media regulator said Yang and Takagi have seven days to explain why their statutory class license should not be cancelled.
Yang and Takagi, described by local media as a couple based in Australia, were charged on April 14 with seven counts of sedition over articles on the website and a Facebook page between October 2013 and February this year.
They were also charged with withholding documents on the website's finances from police.
Charge sheets said articles flagged as seditious derided Chinese nationals and other guest workers in Singapore, while one post on the website "falsely asserted" that a Filipino couple instigated a fracas at a Hindu festival in February.
Some observers have accused the portal of fanning xenophobia in the labour-starved island nation of 5.5 million people, 40 per cent of them foreigners.
If found guilty of making seditious remarks in public, the two can be fined up to SGD 5,000 (USD 3,700) or jailed up to three years, or both, for each charge. They are due back in court for a pre-trial hearing on May 13.