Guardiola made the comment in a press conference in December 2022 after leaving out Phillips for a League Cup tie against Liverpool.
Phillips, who left City to join West Ham on loan in January this year, took Guardiola's comment to heart following the tournament in Qatar.
"After the World Cup was probably the toughest, when Pep came out and said I was overweight. I did not disagree with him but obviously I took a big knock on my confidence and how I felt at City," he said recently.
Asked on Monday if he regretted going public about Phillips' weight, Guardiola said: "Yeah, I'm sorry.
"Once in eight years is not bad. But I'm so sorry. I apologise to him. I do apologise. I'm sorry."
Guardiola claimed he had spoken to Phillips before making the public comment about his weight, saying: "I never, never before I said something here did not speak with the players in that case."
Phillips has endured a miserable time at City since signing from Leeds in 2022 at a time when he was regarded as one of England's emerging stars.
The 28-year-old struggled to break into Guardiola's side, making only two Premier League starts, and is also enduring a difficult loan spell at West Ham.
He handed Bournemouth a goal with his first touch for the club and was sent off for two bookable offences within three minutes in a defeat at Nottingham Forest on Saturday.
Guardiola was talking ahead of Tuesday's Premier League home clash with Brentford, who title-chasing City beat 3-1 on February 5.
City are four points behind leaders Liverpool and Brentford's visit to Manchester represents their game in hand.
The last meeting with Brentford saw City defender Kyle Walker respond angrily to something Neal Maupay, the forward on loan with the Bees from Everton, had said to him in the closing stages.
Walker has suffered issues in his private life of late but Guardiola refused to be drawn on the reason for the clash, saying: "I don't want it but sometimes there is emotions and it happens, and you know that.
"But this is forgotten. It happened, I think they talked and that's all."
Asked how he dealt with players verbally winding him up during his days on the pitch, Guardiola added: "It depended on my mood!
"Listen, in my period in Barcelona I am in the history for having the record of the most yellow cards conceded. All the time it was for talk, talk, talk.
"So it depends, sometimes I controlled myself, sometimes being crazy. People say 'ah, he cannot control'. As a football player I was the same."
