Trescothick has been suffering from a stress-related illness for 18 months. He returned early from the India and Australia tours last year. He was named in England's provisional 30-man Twenty20 World Cup squad this month then said he would be able to go.
Trescothick, though continuing to play for county team Somerset, said on Wednesday he did not feel he was ready to start touring with England again, which will rule him out of England selection until at least the 2008 English season.
"I fully respect the decision Marcus has made, it is completely an individual thing he has had to do," Vaughan told reporters at England's indoor academy in Loughborough, where the team trained because Trent Bridge was waterlogged.
"It can't have been easy for him to say he's not going to tour with England. (But) the last thing I want is for him to come and play too soon because that could have been the end of him," Vaughan said.
"It must be very difficult what he has gone through because I know the one thing that Tres loves doing more than anything is playing cricket for England."
