In a letter to parents at the Holy Spirit Catholic Primary School, seen by the ABC, principal Paula Sellars said Suraj Mattappallil Jose was preparing for mass at the school's church about 4:15pm when he was attacked.
"[Father] Suraj is currently recovering in hospital and hopes to be home later today," Ms Sellars wrote.
"This letter is not to alarm you, but rather keep you informed.
"I have met with [Father] Dave, [Father] Shehan, [Father] Dan and [Father] Adam to check in that they are okay. They will be updating the parish through weekend masses."
In a statement, a Northern Territory Police spokesperson said a 37-year-old man suffered multiple facial injuries after he was allegedly assaulted by a man with a pen on Strele Crescent in Wanguri on Friday afternoon.
The spokesperson said the 38-year-old alleged offender fled the scene on foot before police arrived but he was later arrested in the nearby Casuarina Square shopping centre.
The man was charged with aggravated assault, intentionally causing harm and resisting police.