The Catholic Church has expressed strong opposition to the program. Bloggers comment on the issue.
Tom Martin asks if sex education should be done “in the classroom or behind a tree?” 
No parent is going to have absolute control over the places their children are going to learn about sex and it seems to me that a wise parent would at least want his or her children to be exposed to proper sex education by trained teachers in a controlled school setting rather than learning about sex from a peer behind a tree.
The Pinoy Catholic echoes the official stand of the local clergy and adamantly suggests that sex education should be left to the parents.
A Filipina Mom Blogger points out  that not all parents may know how to discuss sex with their children:
“We can’t assume parents know how to discuss sex openly. Some might be uneducated to understand the anatomy of reproduction and thus fail to grasp natural birth control methods.”
The Catacomb recommends that sex education should be given to the parents instead.
Why not leave these children alone for now.. Or maybe government should try to impose a law of proper parenting, where in parents are given some constant trainings or symposiums that will equip them with proper knowledge in giving their children the right guidance as they grow up. This will prevent not only the exposure of children to the sensitivity of sex but it will also give the parents a better chance to bond with their kids, spending quality time, giving the necessary attention, love and care…
The x-piles believes that those against the sex education program should go after the mass media instead.
The church could have overlooked the real culprit for the alleged generation of sexual perverts – the mass media. Violence and sex are prevalent on many T.V. shows and movies and these are all absorbed by the youth and children as well. All of these have the capacity to change the moral perception of the youth’s developing minds, bringing them to confusion on what is right or wrong.
Meanwhile, Quod Dixit Dixit questions the government's motives for implementing the program.
It is not clear to me whether the government’s move sprung from its idea that overpopulation is one of the root causes of grinding poverty in the Philippines and hence, it must be put into a lower gear. (N.B.: I always assume perhaps with precision that the main roots of poverty in the country are graft and corruption and the unabated abuse and destruction of the environment and natural resources.)
The women's group Gabriela see the program as a step in the right direction .
The Department of Education (DepEd)’s Memorandum No. 26, allowing the use of teaching modules on sex education, could be a positive step, granting that DepEd will conduct an intensive process of consultation with different stakeholders before full implementation. This will ensure that the program is not implemented mechanically, and all arguments are heard. In our part, GABRIELA, Gabriela Women’s Party and SALINLAHI are willing to become part of the consultation process and share our extensive experience in gender and sexuality education with children and parents.
Ducky Paredes, however, believes that the program is as good as dead  with the appointment of Brother Armin Luistro FSC to the post of Secretary of Education by the new Aquino administration.
Is this the end of the UN-funded program for sex education for lour public schools? Probably. One cannot see how a Christian brother can support sex education for elementary and high school students considering that many in the Catholic Church believe that exposing students to learning about sex and sexuality will surely lead to unwanted pregnancies.