In a speech delivered at Southern Cross University on Friday, Mr Turnbull said the more he reflected on gay marriage, the less convinced he was by the arguments against it.
Mr Turnbull questioned the religious grounds for opposition, saying many things labelled a "sin" in the Old Testament do not form part of the modern Australian legal system.
Few would seek to recriminalise homosexual acts or revoke the rights granted homosexual couples under the Same Sex Relationships Act, he said.
The statement that the best parent for a child is its biological parent can be agreed upon generally, but under many circumstances does not apply, Mr Turnbull said.
Same sex couples are able to adopt children in NSW, the ACT, Western Australia and, to a limited extent, Tasmania.
In addition to which, being married does not confer upon a couple the right to adopt.
Third, while marriage is a federal issue, adoption is a state issue.
"We should not miss the opportunity to legislate for civil unions for same sex couples in this parliament," Mr Turnbull said.
"I recognise that will be seen by many as not good enough.
"But it is better than nothing and, as I said in the House last week on another issue, it is a great mistake to allow your conception of the perfect to be the enemy of the good."
Same sex marriage advocacy group Australian Marriage Equality hit out at Mr Turnbull's speech, saying he should know better than to suggest civil unions as a way forward.
Australian Marriage Equality national convenor Alex Greenwich said wherever civil unions have been enacted they entrench discrimination rather than remove it.
"Civil unions may be a politically expedient cop-out for politicians, but they will never be a solution to the acute hurt and discrimination felt by so many same sex couples, their families and their communities," Mr Greenwich said.
Mr Turnbull said counties that legislated for civil unions later went on to support same sex marriage.
"It appears that most jurisdictions which have legislated for gay marriage have first provided for civil unions," Mr Turnbull said.
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