Immigration and Customs Administration agents may have to atone for their sins … after one agent was caught on video shooting a priest in the head with a pepper ball during an ICE protest — but the feds say the footage doesn’t show the full story.

The icy confrontation between federal agents and protesters went down at an ICE detention facility in Broadview, Illinois on September 19 … but the video is only now making the rounds.

Watch the clip … you can see Reverend David Black on the sidewalk, pleading with arms open toward three agents in combat gear standing on the roof … The agents start firing pepper balls at the crowd during the demonstration — one of many over the past weeks protesting the detention and deportation of undocumented immigrants.

DHS Assistant Secretary of Public Affairs Tricia McLaughlin issued a statement Wednesday to TMZ … saying the partial clip doesn’t show the agitators blocking an ICE vehicle from leaving the federal facility, which impeded operations. She said law enforcement repeatedly ordered the agitators to move off federal property so the vehicle could move and they warned force would be used if the agitators did not comply.

Moments later, Mclaughlin said, “rioters began throwing rocks, bottles and launching fireworks at the law enforcement officers on the roof.” She noted Reverend Black “flipped Secretary Kristi Noem and our team the bird when we were there last week.”

Reverend Black spoke about the incident to Religion News Service, saying, “I invited them to repentance. I basically offered an altar call. I invited them to come and receive that salvation, and be part of the kingdom that is coming.” Black added that after he was shot, “We could hear them laughing.”