Manchester United and Manchester City were two of the clubs who voted against proposed changes that will see deadline day fall on the final Thursday before the Premier League kicks off.
In total 14 Premier League clubs voted in favour of the amendment, the minimum needed for the plans to be approved.
The date change is designed to stop clubs beginning with the season with players who are uncertain about their future.
And even though Mourinho agrees business should be concluded before a ball has been kicked, he understands the decision of the Manchester United hierarchy.
"Obviously I am in favour of that [early closure] because I focus just on the training process," admitted the 54-year-old.
"I want to have my squad and work with them and travel with them on pre-season, I don't want to be waiting on late decisions.
"That's the perspective of the coach. There is another perspective, where I can also include myself. I have to share the problems that the board has.
"It's obvious that, when the decision is not uniform around Europe, obviously we are opening an element of disadvantage for English clubs, and that's the reason why Manchester United voted against."
It is yet to be seen whether the rest of Europe will follow suit with the changes but Mourinho is hopeful.
"I hope it goes to the perfect situation, which is to close for every championship."
