The authorities have also barred the airlines from increasing their fares or adding new charges for the scheme.
The ban comes just weeks after the China Air Transport Association said its members did not support the ETS.
The scheme, implemented from 1 January, levies a charge on flights in EU airspace based on carbon emissions.
The scheme has come in for severe criticism not just from China but also from other countries such as the US and Canada.
China has claimed that the plan could cost Chinese airlines 95m euros ($124m, £79m) in extra annual costs.
Analysts said that given the global economic conditions and an uncertain outlook for the travel industry, airlines were wary of the scheme hurting their profits.
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