From what I understand, Taking Refuge must be in the presence of a qualified teacher and/or at least five ordained Sangha members.
In Dzogchen, I believe that Receiving Transmission or the Pointing Out Instructions of the Direct Introduction to the Nature of Mind, automatically includes Refuge.
There are at least four levels of Refuge as well:
Outer: Buddha, Dharma, and Sangha
Inner: Guru, Yidam, and Dakini
Secret: Bindu/Thig-le, Prana/rLung, and Nadi/rTsa
Ultimate or Innermost-Secret: Dharmakaya, Sambhogakaya, and Nirmanakaya