Comelec Commissioner Benjamin Abalos said the decision was made after the nationwide rechecking of records was done in preparation for the validation of all voters in August.
In Metro Manila alone, verifications made by the Parish Pastoral Council for Responsible Voting and barangay leaders have yielded 300,000 "doubtful registation." The verification will continue up the end of July.
Abalos said voters records in the ARMM provinces of Sulu, Tawi-Tawi, Maguindanao, Basilan and Lanao will now be scrapped. Four other municipalities will also have their entire voting list expunged, including Lapu-Lapu City in Cebu.
Abalos said there were many fictitious and double registrations in these areas.
"It is really that bad in ARMM. We just decided to nullify everything. Because of this discovery, from its current voting population of 1.5 million, I expect the number to go down to 1.2 million," he said.
"This time the registration in ARMM will go with a warning for the registrants not to attempt registering twice because we can detect them. In these areas many people will just disguise themselves and try to go to other registration centers," Abalos added.
For the August validation of voters, a P1.2 billion computer software and equipment will be used to take the pictures and fingerprints of each voter and afterwards store them in a Comelec database making double registration impossible, if not easily detected.
Comelec expects to register between 38 million to 40 million voters.
The Comelec chair, however, attributed the inaccuracy more to the massive relocation of squatters in different parts of the metropolis.