The Philippine Human Security Act that comes into effect on Sunday will allow detention of suspects without charge and provides for up to 40 years in jail for anyone convicted of terrorism.
"I pray that the Lord would enlighten the people concerned and Jonas would be found and that the Human Security Act would not be implemented," said Edita Burgos, whose activist son has been missing for over two months.
Jonas Burgos, a member of a left-wing farmers' group in the northern Philippines, is widely believed to have been picked up by a military "black squad" on April 28, and has not been heard of since.
Black squads are usually armed men in civilian clothes or masked men on motorcycles who have been seen picking up left-wing activists or firing at them.
"I believe my son is still alive and I pray that I recover him alive," his mother told Reuters.
"The pain is really unbearable. If it were not for our faith, then I guess we would really break down. Thank God for our faith and thank God for you people out there."
A local human rights group has said about 200 students, trade union and peasant leaders have disappeared since President Gloria Macapagal Arroyo came to power in 2001. More than 800 left-wing activists have been killed during the same period.
A U.N. special rapporteur on extrajudicial killings said in February the military was responsible for many of the deaths.
Last month, a U.S.-based rights group said there was strong evidence of a "dirty war" by the armed forces against activists and the government's failure to prosecute anyone was creating a climate of impunity.
The military has denied the allegations and has blamed Maoist rebels for most of the killings, calling it an internal war.
NOTHING TO FEAR
Arroyo signed the anti-terror legislation into law in March, but postponed its implementation until two months after congressional elections on May 14 to assure the president's political opponents it would not be used against them.
While the legislation was languishing in Congress for 11 years, the Philippines was criticised by the United States and other Western governments as the weak link in the global fight against terrorism.
The country is fighting Islamic militants in the south and communist rebels across the country.
Since 2000, more than 350 Filipinos have died in about 120 bombings blamed on Muslim militants, mostly in the south. The communist rebels do not target civilians but have been known to carry out land mine attacks against security forces.
Besides detention without charges and harsh jail sentences, the law allows security forces to investigate bank accounts of suspected terrorists or organisations used as financial conduits.
Electronic surveillance is also allowed but only after court approval.
"There's nothing to fear if you are not planning anything illegal," said Ricardo Blancaflor, defence undersecretary and the spokesman for the government's anti-terror task force.
He said there were enough safeguards to prevent security forces from abusing the law, adding some law enforcement agencies were complaining the law was too restrictive and could work against them.
One safeguard allows anyone wrongfully detained to receive 500,000 pesos ($10,800) compensation for each day in custody.
Nevertheless, the law is coming in for severe criticism.
"The government already suffers from highly negative public perceptions in regard to its human rights record," Senator Mar Roxas, a former Arroyo ally, said in a statement this week.
"To push the limits further would only breed more fear and anger among the people. Better to err on the side of human rights than to breed tyranny."