A pre-8th Century Buddhist prayer, this phrase is currently used at the beginning and end of Bujinkan training. It's agreed to be a difficult phrase to translate, but here is a good general one:
"Shikin" = this is a buddhist word that was meant to give the rest of the phrase a certain power. Also, according to the kanji 'Shi' means poetry, and 'kin' can mean Gold, so it might also be translated as Golden Poetry. 'Shi' also means 4, and using that the phrase takes on the meaning of 'Four Hearts', as in a compassionate heart which expresses love for everything, a sincere heart that follows the path of right justness, an attuned heart one with nature, and a dedicated heart which is fully committed to any task.
"Haramitsu" = 'Hara' is, of course, the seat of ones Chi (or Qi) and the physical center of the human body. It can be translated as center, heart, dense, etc. 'Mitsu' is best translated as secret, so this part of the phrase can mean Dense Secret or Dense Heart - usually understood as wisdom.
"Daikomyo" = this one was the easiest to translate. 'Dai' is large or big, 'ko' is self, and 'myo' is light. 'Large Self Light' - a blatant reference to enlightenment.
So altogether, remembering it's a prayer, we've got something like: "May the practice of compassion and sincerity open my mind to the possibility that each moment has the possibility to enlighten, and may my dedication foster the development of wisdom."