It said more than 10,000 vaccination teams will begin a month-long programme to immunise children aged between nine months and four years.
The Philippines hopes to eliminate measles by 2008, earlier than the 2012 target set by the World Health Organisation (WHO).
Yolanda Oliveros, director of the department of health's National Center for Disease Prevention and Control was quoted by local media saying all health activities will be halted for a month to ensure the success of the programme.
Although a safe vaccine has been available since 1963, measles remains a leading cause of childhood preventable death and disability.
It is estimated that 20,000 to 30,000 deaths a year in the region are due to measles.