Six coalition MPs raised issues about the Safe Schools program at a partyroom meeting in Canberra on Tuesday.
One MP described it as having a "Marxist agenda", while others added that it should be stripped of its funding.
However, another MP said it was important the children who struggled with their gender identity were supported.
Education Minister Simon Birmingham told the meeting the government should not lose sight of the fact that children were often bullied and harassed as they struggled with their identities.
Mr Turnbull asked Senator Birmingham to report back to him on the operation of the program.
Liberal senator Cory Bernardi has called for the program to be defunded, armed with a petition with more than 9400 signatures to be presented to the Senate on Tuesday.
Senator Bernardi has labelled the program entirely inappropriate and radical.
"Eleven-year-olds should not be persuaded into thinking they are sexually attracted to other people," he told ABC TV.
"What happened to allowing children to be children, to make mistakes, to learn resilience, climb trees, scrape their knees and learn how to deal with each other without being indoctrinated into a program most parents simply don't want."
Labor frontbencher Penny Wong said the program was designed to address the high rates of self-harm and attempted suicide among gay and lesbian youth.
"We all want our children to be safe," she told ABC TV.
"I hope the more sensible people in the Liberal Party will continue to focus on that very important objective."
In a statement, Safe Schools Coalition Australia said it "welcomed all opportunities to demonstrate the positive impact of this important program and provide the facts and evidence behind it".
"This program was developed in response to requests from Australian teachers and principals looking for advice and resources to better support the diversity and well-being of their students and create safe learning environments," the statement read.
"Already, close to 500 schools have opted in to the program, with over 15,000 teachers choosing to utilise the training and tools offered so they feel better equipped to support same sex attracted, intersex and gender diverse students, their families and peers.
"All students, staff and families deserve to feel safe, included and valued at school. Ensuring the well-being of all students and their equal access to education is what this program is all about."
The Australian Christian Lobby welcomed Mr Turnbull's decision.
Their managing director Lyle Shelton said bullying children was unacceptable, but the Safe Schools program went way beyond the purview of an anti-bullying program.
"Parents expect their children to be safe at school but encouraging boys who identify as girls to use the girls bathrooms and share school camp accommodation is not the way to do this," Mr Shelton said.
Mr Shelton said many parliamentarians were unaware of what Safe Schools promotes to children as young as four.
"Telling four-year-olds that no one can tell you what gender you are is confusing and indoctrination in contested and dangerous gender theory," he said.
"Safe Schools tells children they must have access to the Minus 18 website which instructs girls in chest binding so their breasts are flattened and penis tucking for boys."
The Victorian Government plans to make Safe Schools mandatory from 2019.
