The head coach of the under-performing team had been asked a series of questions by Television New Zealand's Thomas Mead, relating to their 2-10 record in this year's Super Rugby Pacific competition.
With the news conference finished but the cameras and microphones still on, Penney made his feelings clear about the exchange.
In a statement on Thursday, Crusaders chief executive Colin Mansbridge said the "private comment" was inadvertently picked up on third-party microphones.
"Rob has since apologised to me for what was said," Mansbridge said.
"On behalf of the Crusaders organisation, I apologise for the comments he made regarding the reporter. I spoke to the reporter today and he has accepted our apology."
Mead had initially asked Penney how much responsibility he was taking as coach, as opposed to his players.
"We're all in it together. It's a combination of many things and we'll endeavour to put on a great performance this week against the Blues," he responded.
Penney said he was "absolutely" expecting to be in the Crusaders head coaching job next year and flatly denied considering walking away from the role that he took over from Scott Robertson this year.
He seemed to take particular umbrage with being asked about having the backing of his playing group, refusing to give any details on any conversations that have been had on the matter.
When asked about if he wanted to "put a line" under the 2024 season, Penney ruled that out and pointed to past results.
"Because I love this group and I know what they're capable of," he said.
"You only have to reflect back to a few seasons ago to I think 2001 when the Crusaders, after winning three in a row, finished 10th. Then they went through unbeaten in 2002. I'm not sure where all this… the doom and gloom is not something we're buying into."
The 10th-placed Crusaders host the table-topping Blues on Saturday night at Apollo Projects Stadium in Christchurch - a loss in that match will finally finish off their faint play-off hopes.
