"I have never heard the report mentioned by you," Chinese Foreign Ministry spokesman Geng Shuang said at a media briefing, when asked about the report by British newspaper Financial Times.
Quoting three officials, the daily said China had been in direct contact with militants in the south-western province, where many of the scheme's most important projects are located.
The 3,000-km-long CPEC is aimed at connecting China and Pakistan with rail, road, pipelines and optical cable fiber network.
Pakistan military has raised a special force to protect thousands of Chinese nationals working on different projects.
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Refuting the Financial Times story, Geng said, "I want to emphasise that the China and Pakistan governments have maintained consultation on the security of CPEC. Pakistan has taken a series of measures on this effectively safeguard the security CPEC and Chinese citizens. China highly appreciates this.
We hope and believe that Pakistan will continue to step up relevant work and maintain and ensure the security of CPEC," he said.
The China-Pakistan Economic Corridor (CPEC) passes through Pakistan-occupied Kashmir (PoK), over which India has conveyed its protests to China.
Pakistan, which is set to be one of the biggest beneficiaries of the infrastructure initiative, is one of the riskiest parts of the world to do business. Last year, 10 local workers were killed by unidentified gunmen while working near Gwadar port, the linchpin of the economic corridor.
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