City winger Mahrez was left out of Sunday’s Community Shield through fears he could fall foul of doping rules.
Mahrez, 28, captained Algeria to the Africa Cup of Nations title in July.
“This is a non-event from the moment the player took the medications after the Africa Cup of Nations,” said FAF.
“It is a problem for Manchester City.”
Guardiola said he was left out of the squad because of the “risk”, as it is unknown what medicine Mahrez took and what it was for.
“The doctors did not have exactly the medicines,” Guardiola said after the match.
“We don’t have what he took. That’s why, for doping control, today was a risk because the doctors didn’t have it. That’s why he wasn’t in the squad to play some minutes.
“Hopefully he will be back next game against West Ham and in the future everything will be normal.”