In an interview with Spanish radio station Cadena Cope broadcast on Friday, Pochettino said Spurs would be using Real's Valdebebas training ground for their preparations for the final against Liverpool in Madrid on June 1.
"We will train at Valdebebas, but we won't sleep there, we'll be at a nearby hotel. We asked to stay there, but [Real Madrid president Florentino Perez] did not want to let us use their facilities," said Pochettino in a light-hearted tone.
"Perhaps he was saying 'the day that you become coach of Madrid you can stay there', it was a subliminal message."
Madrid responded with a firm statement on their official website on Friday, saying they had received no request from Spurs to stay in their facilities and that both Liverpool and Tottenham would be using their training ground before the final.
"Real Madrid are surprised by comments made by Tottenham Hotspur coach Mauricio Pochettino about an alleged request made to our club over his team being able to stay at Real Madrid's residency ahead of the Champions League final," the statement said.
"Real Madrid would like to say that it is completely false that this request was made. Our club has always made itself available to heed the requests of Atletico Madrid, Liverpool, Tottenham, UEFA and the RFEF (Spanish soccer association).
Atletico's Wanda Metropolitano stadium will host the final.
Real's statement added that Liverpool would train at Valdebebas on the morning of the final, with Tottenham training there on May 30 and 31.
Tottenham declined to comment.
Pochettino, who has guided Tottenham to their first ever Champions League final and secured four consecutive top-four finishes in the Premier League, has been linked to a move to Real Madrid in the past.
The Argentine has said he received an offer to coach Madrid last year when Zinedine Zidane resigned from the role, but explained that he turned it down as he had recently committed to a long term contract with Tottenham.
Zidane has since returned to coaching Madrid, while Pochettino has reiterated his commitment to Tottenham.
"There's still a lot of work to do, but of course I am so motivated to stay... and provide Tottenham with what they deserve," Pochettino told talkSPORT on Friday.
(Reporting by Richard Martin; Editing by Catherine Evans)
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