Thompson could be out for between four and six weeks with the calf injury he suffered during Northampton's Guinness Premiership defeat by Gloucester on Saturday.
Even if the more optimistic of those assessments proves correct, 28-year-old Lions front row will be short of match fitness for the opening Test against the All Blacks on November 5.
It is a bitter blow to England, who are reeling from a mounting injury list which threatens to undermine preparations for the matches against New Zealand, South Africa (twice) and Argentina.
A staggering 23 members of a 55-strong party - made up of the elite-player squad and senior national academy - missed training in Loughborough today with injuries of varying severity.
A further five players arrived for the three-day training camp in order to continue their rehabilitation with England medical team.
It is a worrying state of affairs which Dr Simon Kemp, the RFU's head of sports medicine, blames on the growing emphasis on the physical side of the game.
He said: "Our ongoing injury audit, which provides detailed information about injuries over the course of a season, has shown that an average of 25% of players are unfit at any one time.
"We have always seen fluctuations from week to week in this number but this week we have seen an unusual and unprecedented number of injured players with approximately 50% of the elite-player squad/senior national academy squad unfit to train.
"The majority of these injuries this week are the sort of impact related ones that appear to be a consequence of the ferocity off the collisions seen in the modern professional game."
Head coach Andy Robinson remains upbeat even though the fitness problems have cast a cloud over England's opening training camp of the season with the World Cup less than a year away.
"It is unfortunate that we have so many players injured but they are in good hands with both the England and club medical teams and I am hoping that some of them will be available next week," he said.