The warning Thursday to the Chinese and Indian carriers derived from their failure to report their emissions to the national authorities and their missing of an April 30 deadline for handing over sufficient numbers of permits to the national authorities to cover their emissions last year. The European Commission, the Union’s administrative arm, which made the announcement, oversees the system.

Connie Hedegaard, the Union’s commissioner for climate action, said there was no excuse for the airlines to ignore Europe’s system.

“It’s not so that when we make our European laws, then we say they count for everybody except for Chinese and Indians — and that is no different in the aviation sector,” Ms. Hedegaard said. “It shows how controversial and difficult it is to get to the adequately ambitious outcome we need in global aviation.”

Officials from the Chinese Mission to the European Union did not have any comment. The Indian authorities, and officials at Air India and Jet Airways, the other Indian airline accused of violating the Union’s rules, could not be reached for comment.

The resistance by the Chinese and Indian carriers against going along with even the intra-European portion of the emissions regulations is only one of the snags in the Union’s program, which is the world’s most extensive effort to control greenhouse gases like carbon dioxide. It relies on the use of permits for the right to emit at certain levels, essentially requiring producers of greenhouse gases to pay for the right to emit them.

The system was established eight years ago, initially to cover heavy industry in Europe, but it has lately been on the verge of collapse. That is in large part because the weak European economy has somewhat curtailed emissions- producing activity, weakening demand for the permits.

Another factor is that the national authorities gave too many permits away to sectors like the steel industry. Prices are currently at levels too low to force polluters to change to cleaner practices. Ms. Hedegaard issued a report on Thursday showing the surplus of permits on the market had reached a record high.