The poll, which opened Friday, comes as tensions grow in the former British colony over the future of its electoral system, with increasingly vocal calls from residents to be able to choose who can run for the post of chief executive.
But the Global Times daily, which is linked to China's ruling Communist party, accused the pro-democracy advocates who organised the referendum of being politically influenced by the West. It said "overseas supporters have overestimated the effect of an illegal farce".
"Neither China's central government nor the Hong Kong government will admit the results of the poll," it said.
"It would be ridiculous to determine the direction of Hong Kong's political reform with this informal referendum."
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The organisers' use of electronic voting was "tinged with mincing ludicrousness", said the paper, which often takes a nationalist tone, in a typically colourful English editorial.
Beijing faces continuing tensions in Buddhist-majority Tibet and mainly Muslim Xinjiang, and the paper offered a possible clue to its wider concerns: "The country would fall into tumult if all regions conducted similar referendums."
"The opposition in Hong Kong should not have the delusion that they could, by organising a street farce, achieve what London at the time was not able to do despite making every effort possible," it said.
No reference to the former British administration was included in the article's English version.
The paper accused organisers of having a "gambling mentality", saying that Beijing will "never compromise on sovereignty-related issues".