A national emergency alert system that will send messages to cellphones during disasters is set to be launched in New York City and Washington by the end of year.

The chairman of the Federal Communications Commission, Julius Genachowski, said the Commercial Mobile Alert System will direct messages to cellphones in case of a terrorist attack, natural disaster, or other serious emergency. The plan was approved by Congress in 2006.

Genachowski and FEMA administrator Craig Fugate said the new system will be selective. “These are really focused on the highest levels of alerts, and those that require urgent action,’’ he said.