The websites of at least five government agencies, including the anti-graft office of the government Ombudsman, have been hacked by a group calling itself "Anonymous Philippines", said Roy Espiritu of the science department's IT section.
The message called on the public to join a protest at the gates of the Philippine legislature on Tuesday -- the latest Internet appeal for such demonstrations as anger grows over official corruption.
The hackers condemned "this false democracy (and) this government and the politicians who only think about themselves".
In August an appeal for an anti-graft street protest, aired on social media like Twitter and Facebook, drew tens of thousands of protesters to a central park in Manila. Several smaller protests, also publicized via Internet, have since been held.
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Anger has grown since a newspaper in August reported that a businesswoman connived with opposition legislators to syphon off some 10 billion pesos (USD 230 million) from a special fund allocated to the pet projects of lawmakers.
The businesswoman has been jailed as graft charges are readied against her while the Justice Department has asked for the cancellation of the passports of three opposition senators and their alleged conspirators.
In response, Aquino went on national television last Wednesday to declare "I am not a thief". He accused the opposition of trying to divert public attention from their own alleged corruption.
Previous hacking attacks on Philippine government websites have been the work of foreign groups angry over diplomatic disputes or -- as in September 2012 -- by those angry at a restrictive cybercrime law.
"There is forensic work being done on our end to find out who did this because it is still a crime," Espiritu said.
However since government agencies maintain individual websites with no uniform standards, it is difficult to secure them from hacking, Espiritu said.