The International Olympic Committee's (IOC) Evaluation Commission are visiting the Spanish capital week after having already travelled to Chicago, Tokyo and Rio.
Insidethegames had revealed on Sunday how Rio organisers had stripped Simon Walsh, a British-based freelance journalist and consultant who also works on Madrid's bid, of his credentials after they learned he had been accredited through EFE, the Spanish-state run news agency.
Rio organisers are currently considering reporting Madrid to the IOC's Ethics Commission.
They have already written to the IOC Evaluation Commission to complain about the conduct of Madrid.
Malcolm Munro, Madrid's international media director, said: "[We] weren't spying, weren't trying to unveil secrets, [we] just wanted to see how this thing works so we could organise the best possible one for the media [here].
"The whole thing has got out of proportion, really.''
Munro said the whole event was a misunderstanding with Madrid making a mistake not to have been transparent from the start.
Although he accepted that the situation could have handled better, Munro did not believe Rio would report Madrid to the IOC.
He said: "I think this thing is quite commonplace and nobody intends to underhand."
Madrid would welcome any media specialists working with rival bids, he added.
The IOC's 13-member team arrived yesterday for the five-day tour.
The IOC are due to announce the winner at its Session in Copenhagen on October 2.