Marseille coach Marcelo Bielsa insists he was always fair with summer signing Doria, who departed the club last week.
Doria, 20, failed to make a first-team appearance following his arrival from Botafogo for a reported fee of seven million euros, and has joined Sao Paulo on loan with an option for a permanent transfer.
Upon his unveiling back in his homeland, the Brazilian defender told reporters: "Marcelo Bielsa? I don't want to speak about him because he never spoke about me."
Bielsa, addressing the French media at his press conference ahead of Friday's game against Reims, rejected that suggestion, with L'Equipe quoting him as saying: "Publicly, I have always spoken of him in good terms.
"In no way can I allow myself to make decisions which prevent a player from developing with the club based on differences on his arrival.
"I have described the manner of his arrival. I was not consulted and did not know him well. But from the moment he began working with us, I have worked hard with him."
Dória veste a camisa e avisa: "Estou pronto" http://t.co/lM6tu9XjGP pic.twitter.com/HuRhnWGbZX
- São Paulo FC (@SaoPauloFC) February 9, 2015
Jeremy Morel, Nicolas Nkoulou and Rod Fanni have been the established starters in the centre of OM's defence this season, with fellow youngster Baptiste Aloe also preferred to Doria.
"Every time we play, 10 staff members analyse the match and each player receives a rating," said Bielsa. "The three players with the best average ratings are Nkoulou, Morel and Fanni -- the three central defenders who have played.
"When they have not played, Aloe has played because I thought he could best help the team. Aloe has received a mark of seven in each of his games. So should I have played Doria in his place, against all my criteria?"
Doria was also unhappy at being played out of position at left-back in a reserve-team game.
But Bielsa continued: "The first thing I said to him was not to preoccupy himself with positions because in our team: the left-sided central defender ends up playing a lot at left-back because of Benjamin Mendy's attacking tendencies. My decisions are always taken solely for the benefit of the team."
Bielsa also had to deal with an on-field altercation between playmakers Dimitri Payet and Florian Thauvin during Saturday's draw with Rennes.
He said: "That sort of thing happens occasionally but I did not intervene. It has not caused problems in the long term.
"When I talk about my preference for training sessions behind closed doors it is because of this type of episode, which is commonplace but generates a lot of attention in the media.''
Full-back Brice Dja Djedje added: "Flo and Dimi are big boys. I had a few words myself with [Andre-Pierre] Gignac and Nico Nkoulou.
"These things happen in all teams, it's nothing to worry about. They are not bad boys."