Confession of misdeeds enables us to purify the temporary stains, obscurations and habitual tendencies that obscure our Buddha nature. Broken samaya vows especially can hinder our progress on the path. The Vajrayana path of skillful means stresses the importance of immediately and openly proclaiming one’s mistakes and resolving not to repeat them.
We can find many confession practices, most notably those associated with Vajrasattva. Probably the most famous confession in our tradition is the Narak Kong Shak. The full name of the text is Narak Dongtruk (Emptying the Lower Realms from their Very Depths): The Sovereign Practice for the Confessions of all Violations and Breakages, Negative Actions and Obscurations.
This profound practice includes refuge and prostrations before the hundred peaceful and wrathful deities. It also features confession while resting in the view, and offering practices. Because it is so effective, Phakchok Rinpoche has encouraged students to practice this confession regularly–at least once a month.
We can insert the confession after the mantra recitation in any sādhana we may be doing. Then we return to conclude the sādhana and do dedications and aspirations.
In this audio recording Phakchok Rinpoche leads a group in this lamenting apology. He also gives a brief explanation of each section of the practice .
You might also be interested in this commentary on the Narak Kong Shak confession practice.