This sounds like the novel Abduction by Robin Cook from 2000.
Points that match:
underground civilization, which is highly advanced, very peaceful, very sincere where no crime is present.
Check. "They discover a technologically advanced world of genetically engineered, physically near-perfect humans living comfortably in an enclosed city within the Mohorovičić discontinuity. "
Moral values and rules were different and soon complications started to happen with the Earth visitors.
Check. Sexual mores are different which causes a major complication with the surface visitors.
This civilization was discovered by mistake, by either a geological tour, or some kind of trip where they stumble through a cave opening then enter it.
Check. A team of researchers in a remote region of the Atlantic become trapped inside an ancient undersea volcano when their submersible is inexplicably drawn in.
It is highly enjoyable and I was very intrigued by it. I do recall that the author was a doctor, or physician but then again I may be wrong,
Check. Robin Cook was a physician by training and has written several dozen medical thrillers.
it’s been more than 20 years since I've read it.
Check. Published in 2000 so just over 20 years ago.