China has rejected 545,000 tons of imported US corn found to contain an unapproved genetically modified strain.
An unapproved strain called MIR162 was found in 12 batches of corn, China's product safety agency said.
China backs genetically modified crops to increase food production, but has faced opposition from critics who question their safety.
The agency called on US authorities to tighten controls to ensure unapproved strains are not sent to China.
China allowed its first imports of a genetically modified crop, soybeans, in 1997. Authorities are trying to develop others that produce bigger yields or can resist insects without use of pesticides.
China has already approved 15 varieties of genetically-modified corn for imports and MIR162 is awaiting approval.
"The safety evaluation process [for MIR162] has not been completed and no imports are allowed at the moment before the safety certificate is issued," said China's vice agricultural minister, Niu Dun.
The Ministry of Agriculture has recently launched a publicity campaign to allay concerns over GM foods and says the criticisms are unfounded.
The first batch of corn was rejected in November after authorities detected MIR162.