This is mentioned in the Great Treatise on the Stages of the Path to Enlightenment, Volume 1 Page 246 - 247:
“Thus, having understood virtuous and nonvirtuous karma and their effects, do not leave it at just an understanding but meditate on it over and over, because this is a very obscure subject and it is difficult to acquire certainty about it.”
Here, it refers to karma as a “very obscure subject”, which is the same meaning as what you mentioned in your post. In Chinese, we call it “极隐秘法”, where you just have to rely on faith in the Buddha words. Therefore, the text continues,
“Further, the King of Concentrations Sutra says:
Were the moon and the stars to fall from their place
And the earth with its mountains and cities to perish
Or the realm of the sky to completely transform,
You [Buddha] still would not speak a word of untruth”
The text goes on the rebuke those who claim to have acquired certain knowledge of emptiness, but are uncertain about karma and its effects.
His Holiness, The Dalai Lama’s advice on this is to develop respect and faith for the Buddha first by meditating on His good qualities.
We should also study, analyse and meditate upon those teachings that we can understand through logical reasoning and experience(interestingly, His Holiness said emptiness is one of these). When we analysed these teachings deeply and see how they coincide with our own experience in life, we gain a confidence in them that is based on our own reflections. This develop faith in the teachings, and we will come to feel that since the Buddha gave such profound, logical instructions that are true, then surely his other doctrines will be correct.
My own experience is also the same. So far, those teachings that I can study, analysed and put into practice are as what the Buddha said, and they also changed my life for the better. Even just living my life based on karma being the truth makes me a happier person. Furthermore, the doctrine of karma doesn’t contradict the other truths, so there is no reason to doubt the truth of it, even though I couldn’t directly prove it through reasoning or experience.