The 21-year-old has been a key target for the Premier League champions throughout the summer, with previous bids of £20 million and £26m rejected, and are confident of closing in on a £30m deal this week.
Martinez is unhappy that the window is still open when the season has started, with transfers possible for English clubs until September 1, following Everton's 2-2 draw with newly promoted Watford on Saturday.
"The window, when it is open and we have to prepare for official games, is very, very unfair. I don't think it is right," he told Sky Sports.
"I think we should have a period where we assemble our squad, and then once the first league game starts everyone is focused.
"I think we forget that footballers have a human side and it can really affect. Players like Stones and [Ross] Barkley have an incredible future and will attract interest from the outside."
The nature of Chelsea's pursuit for Stones has caused some friction between the two clubs, as well as Jose Mourinho and Martinez, with the Portuguese going public with his interest in July.
