Vaughan, for whom missing the rest of the English season would not be the worst diagnosis, has not played for England since being forced home early from the tour of India in March.
His right knee injury flared up again during last week's County Championship match between Yorkshire and Sussex at Arundel where the 31-year-old Vaughan was unable to field for most of the game.
Afterwards, Yorkshire physio Scott McAllister said: "Michael's rehab programme seems to have suffered a setback.
"A fourth operation on his knee is a possibility but at this stage nothing has been set in stone and the situation needs to be carefully assessed."
Another attempt at keyhole surgery to clear away internal debris would sideline Vaughan for at least 10 weeks.
That would rule him out of the four-Test series against Pakistan starting next month.
But were Vaughan to have a major operation to repair a hole in the surface of his knee joint he might be out for as long as nine months.
That would end his hopes of captaining England in Australia and at the 2007 World Cup in the Caribbean.
Vaughan, who led England to Ashes glory last year, played the last of his 64 Tests against Pakistan at Lahore in December. He has so far scored 4,595 Test runs at an average of 42.94 with 15 hundreds and a best of 197.
The England skipper is one of several senior players on the team's injury list with all-rounder Andrew Flintoff (ankle), left-arm spinner Ashley Giles, and fast bowlers Simon Jones (knee) and James Anderson (back) also ruled out of the ongoing one-day series with Sri Lanka.
Flintoff, Andrew Strauss and Marcus Trescothick have all filled in while Vaughan has been out of action and they remain the leading candidates to take over if the selectors have to pick a new permanent captain.
England are currently 4-0 down against Sri Lanka in a five-match one-day series heading into Saturday's Headingley finale after, in Vaughan's absence, being pegged back to a 1-1 home Test series draw by Mahela Jayawardene's men.