"We have to retract the media statement by the ASEAN (Association of Southeast Asian Nations) foreign ministers... as there are urgent amendments to be made," a Malaysian foreign ministry spokeswoman said.
She said the ASEAN Secretariat approved the release of the statement, then later informed the ministry it was being retracted.
The ministry had released a statement hours earlier following a meeting of the Chinese and ASEAN foreign ministers -- hosted by China -- that appeared to rebuke Beijing over its actions in the waterway.
It was not immediately clear why the statement, whose wording was in line with recent statements by ASEAN, would need to retracted.
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China claims nearly all of the South China Sea -- a vast tract of water through which a huge chunk of global shipping passes.
It has bolstered its claim by building artificial islands including airstrips in the area, some of which are suitable for military use.
The region is bracing for a ruling by a UN tribunal on a claim brought by the Philippines against China.
China does not recognise the arbitration and has reacted angrily to the Philippines' legal efforts over the Beijing-controlled Scarborough Shoal, off the main Philippine island of Luzon.