This allegation has two parts. The first is about Freemasonry's basic approach to religion. Freemasonry is not a church, a sect or a religious denomination. It has no creed, no cult and no sacraments. The RCC is wise enough to recognize this, but they claim that the rituals and principles of Freemasonry "embody" or "are based upon" a naturalistic religion -- which is incompatible with Christianity. So what is "naturalism"?
Naturalism is a philosophical standpoint which claims that nothing exists outside nature. In other words, if God exists, he is part of nature and subject to its laws. This is in conflict with Christianity, which claims that God exists outside creation, outside the visible and researchable nature in which mankind lives. God is supernatural.
I have not seen any of the documentation which one must assume underlies the allegation, just the conclusion itself. It is possible that naturalistic ideas can be found in some Masonic writings. Over the nearly 300 years of Masonic history, many different ideas and fads have affected it to some degree. Yet in present-day Freemasonry, I have not encountered any writings or persons making naturalism a Masonic issue.
The second part of the allegation is easier to deal with. It is a conclusion easily jumped to when one finds out that Freemasonry welcomes men of different religions. The idea that all religions are equally true and equally valid ways to God, and that in consequence one should ignore the differences and amalgamate all religions into one single worship of "the brotherhood of man and the fatherhood of God" -- is usually called Deism.
Freemasonry holds no such belief or opinion. It makes no attempt to change the religion of its members in any way. It makes no comment on the relative veracity of religions. Its doctrine on religion has a completely different cause and goal.
Freemasonry accepts as members men who believe in a divine Creator who will judge us after our earthly life. The reason for this is the conviction that only those who have such a belief can be trusted. With Dostojevsky, they say "without God, anything is permissible". A man who does not believe in God and the possibility of divine retribution, feels free to do anything as long as he gets away with it.