The goalkeeper told Marca that he felt "half-Spanish", bringing into question the 24-year-old's commitment for the second time in six months - back in May he suggested he wouldn't end his career at Chelsea.
Antonio Conte has little patience for players who disrupt his squad, but Courtois is working to convince his manager and fans that he is not Chelsea's trouble maker
The 24-year-old's agent, Christophe Henrotay, told Goal: "Courtois is happy at Chelsea, he is playing well and he is going nowhere.
"Sometimes when you do an interview that is not recorded on video then it can be portrayed wrongly, he didn't mean to give that message and isn't looking to Spain."
Henrotay was referring to his client's comments about Atletico Madrid, where the Belgium No.1 spent three years on loan, appearing to signal that he wanted a return to La Liga.
"The three seasons at Atletico made me the goalkeeper I am now," Courtois has said. "When I said goodbye, I left Spain knowing that one day I would return there.
"I have a contract with Chelsea for three more seasons. In 2018, when I enter the last year of my contract, we will have to weigh up whether it is best to renew or leave."
He went on to reveal that Real Madrid been in contact with him while he was injured as they sent the Chelsea's club fax machine at Cobham training ground.
Chelsea's fans reacted negatively to the quotes, which came out while their side hit a rough patch in the league and were preparing to face title rivals Arsenal, who happened to have the Blues's greatest ever goalkeeper, Petr Cech, playing for them.
Meanwhile, Conte chose to swap goalkeeping coaches upon his arrival, from Cech's mentor Christophe Lollichon to Gianluca Spinelli, on the request of Courtois after he fell out with Lollichon last season.
With that in mind, it was puzzling why Courtois had made those comments as he appeared happy at Stamford Bridge and senior staff sought an explanation for his comments.
It was agreed that they were misrepresented so Courtois decided to clarify his position after his side's 2-0 win over Hull City in the Premier League last weekend.
“I understand the commotion with the Chelsea fans,” said Courtois. “But I just meant that I want to return to Spain one day – but it can also be after my career.
“I’m happy to be at Chelsea. For how long, we will see. But now I want to win prizes with this club.”
The shot-stopper is away on international duty right now and will face off against his Chelsea rival Asmir Begovic on Friday as Belgium take on Bosnia & Herzegovina.
Courtois must be wary of saying anything else that could alienate him considering the hugely talented Begovic is waiting for his chance to usurp him.
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