President Benigno Aquino's spokesman Abigail Valte appealed for a stop to the attacks, on the websites and social media accounts of the weather service, the earthquake and tsunami monitoring service and the social welfare agency.
Valte did not disclose the extent of the damage, if any. All the sites she mentioned appeared to be up and working again.
"Many people are being affected by this," she said.
"We are aware of the opposition to the National Cybercrime Prevention Act. There are other ways to express opposition to it," she said in an appeal broadcast on government radio.
The Philippines sits on the "ring of fire" of tectonic activity that generates earthquakes around the Pacific, and is also regularly hit by typhoons, with the agencies' online services providing citizens with disaster data and advice.
Valte reported the attacks a day after Aquino set out a broad defence of the cybercrime law, which seeks to stamp out offences such as fraud, identity theft, spamming and child pornography.
But it has sparked a storm of protests from critics who say it will severely curb Internet freedoms and intimidate people into self-censorship.
One of its most controversial elements mandates much longer jail sentences for people who post defamatory comments online than those who commit libel in traditional media.
It also allows the government to monitor online activities, such as e-mail, video chats and instant messaging, without a warrant, and to close down websites it deems to be involved in criminal activities.
The Supreme Court is hearing petitions to have the law declared illegal.
Aquino, whose mother led the "people power" revolution that toppled the military-backed Ferdinand Marcos regime in 1986, said he remained committed to freedom of speech.
But he said those freedoms were not unlimited.
Source: AFP via I-Net Bridge
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