The agreement was reached by the defense ministers of the two countries in May but Beijing missed August and Dec. 31 deadlines for establishing the hot line, the official said, speaking on condition of anonymity due to the sensitivity of the issue.
The agreement, aimed at boosting exchanges of intelligence between the sides, came after North Korea detonated a nuclear device in October 2006.
"China had agreed to establish the hot line before the end of last year, but it has missed the target date," the official said.
A military attache at the South Korean Embassy in Beijing has paid a protest visit to the Chinese government, the official added, without identifying which government office was visited.
Defense Ministry officials said the delay was caused by the Chinese government's refusal to approve the establishment of the hotline, noting the militaries of the two countries have already worked out details for its establishment.