After weeks of intense lobbying, the Senate today began considering a private member's bill from former health minister Kay Patterson that seeks to overturn a ban on producing embryos for stem cell research.
Mr Howard had allowed parliament to hold a conscience vote on the issue, so MPs are not bound to follow party directives.
"I am wrestling with this issue," Mr Howard told reporters.
"On the one hand I want to do everything possible to help relieve suffering and to leave open the hope of cures for terrible debilitating illnesses.
"On the other hand, I do have concerns that this may in some areas be a step too far.
"I am still weighing the matter. I envy those people who think it's so simple.
"Some of these things aren't so simple as people pretend."
Emotional debate
Existing stem cell laws limit scientists to using surplus sperm-and-egg embryos left over from IVF procedures.
Advocates of stem cell research say it offers potential medical breakthroughs, while opponents raise ethical concerns about creating cloned embryos and then destroying them in the name of science.
In the first four hours of debate, which precedes a rare conscience vote on the issue, 10 senators spoke in favour of passing the bill and six opposed it.
Victorian Liberal Mitch Fifield said he would not support the bill because it allowed the creation of cloned human embryos that had the potential to become human beings.
"I understand and accept that no one is proposing that any of these new sorts of embryos be implanted into a woman," he said.
"Even if they were, they would be unlikely to thrive. But I cannot cross the line to create cloned human embryos that have the theoretical potential to become cloned human beings."
Liberal senator Gary Humphries went further, suggesting that passing the bill would put scientists on a slippery slope to human cloning, as embryos would have potential for independent existence.
"The clear ethical boundary we seek will be behind us, not in front of us," Senator Humphries said.
Greens senator Kerry Nettle foreshadowed an amendment calling for a stem cell bank to be established within two years to ensure the public could benefit from research.
Liberal senator Judith Troeth accused opponents of the bill of using dirty tactics and making false claims about what the legislation would allow.
The bill did not permit human reproductive cloning and prohibited the development of human-animal hybrids, Senator Troeth said.
The proposed laws closely follow the recommendations of the expert Lockhart review, which earlier this year said the ban on therapeutic cloning should be changed.
Thirty-six hours have been set aside for debate and a vote will be taken before the Senate rises on Friday.