The health department said in December it would give out contraceptives in schools as part of a strategy to prevent HIV infections, prompting criticism from some lawmakers and bishops in the mainly Catholic nation.
The Philippines has a rapidly growing HIV epidemic, with rights groups saying the government has failed to promote contraceptives and give sex education to gay or bisexual men.
However the education department said this week it would not allow condom distribution in primary and high schools because laws only mandated the agency to provide "sexuality education".
"We want to be sensitive to what the parents feel and we got the feedback that they don't agree with the idea," education assistant secretary Tonisito Umali told AFP.
"Parents think this will send a wrong signal to our students that it's OK to have premarital sex, to have sex while you're a minor so long as you are protected."
Access to contraceptives is a contentious issue in the Philippines, with the influential Catholic Church opposing laws and programs seeking to distribute condoms to the poor.
President Rodrigo Duterte has challenged the Church, ordering government agencies last month to deliver free contraceptives to six million women to boost a family planning program.
His health department has also launched a plan to curb the spread of HIV especially among Filipinos aged 15 to 24, which it said was the most vulnerable to infection.
Health department spokesman Eric Tayag said his agency would continue distributing condoms in clinics and outreach missions despite the decision of the education ministry.
"We're not disappointed because one big thing that happened was we mainstreamed the conversation about condom access, which was taboo before," Tayag told AFP.
Filipinos aged 15 to 24 are the most vulnerable to HIV infection. Source: AAP
Tayag added critics had confused HIV prevention with family planning.
"HIV in the Philippines mostly happens when you have unsafe sex: males having sex with males. Nobody gets pregnant among that vulnerable group," he said.
"For those who have already experienced sex, we are aiming for risk reduction and one (way) is condom access."
The Catholic Bishops' Conference of the Philippines said giving students condoms was "a waste of public funds".
