Asking a question to try and clarify your question.

The two groups I know that refer to their organization as "The Church" are Mormons and sometimes Catholics. To what church are you refering to?

I do not know anything about catholicism but I do believe I can answer your question about it with regards to mormonism.

“Masturbation, a rather common indiscretion, is not approved of the Lord nor of his church, regardless of what may have been said by others whose ‘norms’ are lower. Latter-day Saints are urged to avoid this practice. Anyone fettered by this weakness should abandon the habit before he goes on a mission or receives the holy priesthood or goes in the temple for his blessings.” (Spencer W. Kimball, “Love Versus Lust,” Brigham Young University Speeches of the Year [Provo, 5 Jan. 1965], p. 22.)

This is a qoute from President Kimball at a BYU speech.

In order to get an idea as to why the Mormon Church holds the beliefs that it does is to look back on the prevailing idea of the time.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1071473/

This article illustrates that during the time of the Mormon Church's formation, the victorian ideals that were in vogue at the time in conjunction with falacious science led to the wide spread and popular belief that masturbation was not only immoral but could even lead to insanity.

It is reasonable to assume that, since the ideals of the time held it to be wrong morally and that the science of the time thought that it caused insanity, anyone of the time would attribute this to God as being the source of the belief that masturbation is wrong.

When it comes to an organization such as the Mormon church where in every leader is believed to have communed directly with God on all major decisions, it makes it very hard for any kind of change to occur on moral views such as this.

The fact that the rest of society has passed them by on the subject of masturbation being immoral has only cemented the view in their mind. Since they believe the temptation to masturbate, or break the law of chastity in general, is caused directly from the devil, and that anyone outside of the church is believed to lack the moral guidance neccessary to follow Gods will. The rest of society becoming ok with mastutbation merely enforces the depth to which they believe not masturbating is necessary.

https://www.lds.org/manual/gospel-principles/chapter-39-the-law-of-chastity?lang=eng

If you are coming from the stand point of being a current member of The Church then it is important for me to prove to you that other aspects of the Church's beliefs are derived from the prevailing ideas of the time.

The LDS church was formed in an area of NY known to historians as the "Burned Over District" due to the propensity for new cults and religions to spring up during the second great awakening.

The word of wisdom contains within it guidelines which also folloe the prevailing theories regarding what is and isnt safe to put in our bodies. While it has proven true for many aspects one aspect it has not is regarding "hot drinks". The word of wisdom states that "hot drinks" are not to be consumed. While today this has been interpreted as meaning Coffee and Tea (pick me up drinks), at the time Joseph smith wrote it, it was believed that hot drinks actually damaged your stomach.

One aspect that the Church has admitted was a product of the prevailing ideas of the time is the ban on blacks from holding the priesthood and entering the temple, which therefore bans them from salvation.

The church has since admitted this was instituted by prophets speaking as men and not with the word of God.

So if these things could be influenced by the prevailing ideas of the time. Why not masturbation?