Le Luong Minh, ASEAN secretary-general and a veteran Vietnamese diplomat, told the Manila Times last week that the grouping rejects China's policy of using the dotted line to assert its sovereignty over myriad islets and reefs in the sea.
ASEAN's economic integration could also be affected by "any hostility or conflict" that could break out, he added.
Vietnam has repeatedly complained about what it sees as aggressive Chinese moves in the seas.
Chinese Foreign Ministry spokesman Hong Lei said that China had always supported ASEAN's economic integration, but that ASEAN was not a party to the South China Sea dispute.
"Mr. Le Luong Minh is the ASEAN secretary-general, and on the South China Sea issue has many times made partisan statements that do not accord with the facts nor suit his position," Hong told a daily news briefing.
"This is a serious deviation from the neutral position ASEAN and its secretary-general ought to have on the relevant issue, and damages the image of ASEAN as a regional international organisation," he added.
The secretary-general should ensure ASEAN stands by its promises of neutrality and not "use public office for private gain", Hong said.
It was not clear why China had waited so long to respond to the remarks, which were published last Wednesday.
China claims about 90 percent of the South China Sea, displaying its reach on official maps with its nine-dash line that stretches deep into the maritime heart of Southeast Asia.
Vietnam, the Philippines, Malaysia, Brunei and Taiwan also have claims to parts of the potentially energy-rich waters that are crossed by key global shipping lanes.
Chinese Foreign Minister Wang Yi (R) holds talks with Le Luong Minh, Secretary-General of Association of Southeast Asian Nations (ASEAN), in Beijing, capital of China, Oct. 17, 2013.