The Manchester City boss criticised the quality of the Mitre Ultimax Pro ball after his side booked their place in the quarter-finals.
A brace from Nico O'Reilly and a strike from Kevin De Bruyne saw City come from behind to beat Plymouth 3-1 on Saturday.
However, it could have been more comfortable, with the hosts firing 20 of their 29 shots off target.
Guardiola put those wayward efforts down to the Mitre match ball after the cup tie at the Etihad Stadium.
He explained: "The ball in the Champions League is exceptional, the ball in the Premier League is exceptional, this one isn't. It's difficult to control.
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"When you lose it [sounds like] you're complaining, but the ball is not right. In many years it's happened in the FA Cup and Carabao Cup, I know it's a business and they come to agreements.
"You know how many shots went over? Look at other games. Normally the ball goes inside from these shots."
The FA have now issued a response to Guardiola's comments.
A spokesperson said: "Mitre's Ultimax Pro ball - used in the Emirates FA Cup and all other FA competitions - has been tested in accordance with FIFA testing.
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"All footballs in the professional game are required to meet the FIFA Quality pro accreditation, and this ball delivers against all of the testing requirements.
"Alongside Mitre, we understand that preference is subjective, but we're confident that the ball performs well.
"With over 350 goals scored in the knockout competition so far, it provides an exciting element to such a competitive tournament."
Despite Guardiola's issues with the ball, City are into the last eight of the competition for the seventh season in a row.
The seven-time winners have been drawn away to Bournemouth in the quarter-finals, with the tie to be played on the weekend of March 29.
Guardiola is not the only Premier League manager to make comments about a match ball.
Mikel Arteta took aim at the Carabao Cup's Puma ball following Arsenal's semi-final first leg loss to Newcastle.
The Gunners boss said: "We kicked a lot of balls over the bar, and it's tricky that these balls fly a lot."
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In response, the EFL explained that the ball complied with the highest FIFA standards.
It was also highlighted that the same ball has been used in Serie A, LaLiga and the three EFL divisions.