At the awards, presenters Warren Beatty and Faye Dunaway named La La Land as the winner in the Best Picture category, when Moonlight had actually scooped the prize.
During the La La Land acceptance speech the mistake was corrected and the actual winner was announced.
In a statement published by the Academy's website soon after the event, PwC said: "We sincerely apologise to Moonlight, La La Land, Warren Beatty, Faye Dunaway, and Oscar viewers for the error that was made during the award announcement for Best Picture."
"The presenters had mistakenly been given the wrong category envelope and when discovered, was immediately corrected," the PwC statement said.
"We are currently investigating how this could have happened, and deeply regret that this occurred."
The firm has handled the ballot-counting process for the past 83 years, a spokesperson for the company told PRWeek, but declined to comment further on the situation.
Only two of its current employees - Martha Ruiz and Brian Cullinan - count each individual vote and know the names of the winners before they are announced.
Ruiz and Cullinan are also responsible for award-winners' envelopes as they are escorted to the ceremony, as reported by the BBC. Its article last week about the process was one of several to appear across international media, in something of a PR coup for the professional services firm.
Former broadcast journalist Michaela Gray, who is currently a media trainer and account manager at PR firm Golin, said there was one correct way to handle live TV crisis comms.
"In broadcast, a moment is there and gone, so make a no-fuss but sincere correction and move on quickly. Broadcast time is too limited to fight over who you are or why you're there," Gray said.
Gray added that the gaffe was unlikely to have a big dent in PwC's reputation amongst their primary business audience.
Following the error, La La Land lead actor Emma Stone addressed reporters and said the cast was "so excited" for Moonlight, though offered no explanation as to how the mix-up occurred.
In a similar incident at the 2015 Miss Universe contest, host Steve Harvey read out the wrong name and was forced to remove the crown from Miss Colombia and hand it to the actual winner, Miss Philippines.
Several brands have made light of the situation on Twitter.