As his international teammates made 318 for three on the first day of the first Test at Lord's here Thursday, Vaughan was discovering that his right knee was not yet ready to withstand the rigours of first-class cricket.
The 31-year-old batsman, who has not played since quitting the tour of India earlier this year on the eve of the first Test in Nagpur had hoped to feature for Yorkshire this week.
Two weeks ago it was getting to the stage that I was close to playing," Vaughan said.
"This Sunday against Northants in the C and G (One-day tournament) was potentially a chance of me playing. But there was a little bit of a setback - when you have rehab and you're working hard then you get the odd setback.
"If I miss another two weeks of the season because of that and it makes me stronger for it, it will be a good decision."
A piece of bone in the joint has created a hole, and until that smoothes over a comeback is not an issue.
For Vaughan to feature in a Test against Sri Lanka he would need to play a four-day game and the only fixture where he can do that - before the back-to-back second and concluding third Tests start on May 25 - is the Roses match against Lancashire commencing Tuesday.
"As everyone knows, it is slow progress. But it looks like progress in the right direction," said Vaughan. "I have batted in the nets, but it is frustrating that I can bat in the nets but not out in the middle.
"I have worked pretty hard and I hope I will get the rewards eventually," added Vaughan, whose position as England captain continues to be filled by star all-rounder Andrew Flintoff.
"I have got to be patient - everyone has to be patient with the knee because when I do come back I want it to be with confidence and for a long time, not just for a short period.
"It is very difficult to put a time span on it. I have to tick all the right boxes to make sure I can withstand a real tough game of cricket. Until I have ticked all the boxes, I will not put myself forward for a game."
Vaughan has not played an international match since leaving the tour of Pakistan to undergo surgery on the joint for the third time in December.
He later admitted the injury was made worse by trying to return for the Test series in India, hence his reluctance to rush back now.
"At the minute I have not been able to twist and turn at pace," Vaughan said. "I can do it at 50 or 60 percent but I cannot get in and out at pace without feeling a little bit of aggravation.
"The last thing I need and everyone else needs is to see a limping Michael Vaughan, like in Pakistan.
"There are a couple of shots, more so on the back foot, when you are cutting the ball for example and putting a little bit more weight on the right knee which is still causing me a little bit of pain.
"If it was just pain I would have a tablet and get on and play; it is the actual aggravation, the locking sensation which is the hard thing to get over. "There is damage in there now, but the specialists I have been speaking to have told me that will get better over time.
"All the training I am doing is towards making sure I can withstand that. I have actually got muscles in my legs for the first time for a long time.
"You might have to get a microscope to see them - but they are there!" he joked.