Vaughan suffered the injury in England's second game - and only win - of the tri-series and was only expected to miss a week.
However, the injury has taken longer than expected to heal. and although England management said he was close to playing Tuesday against New Zealand, wicketkeeper Paul Nixon revealed he was unlikely to play any more part.
England need to win their final two tri-series games to have any hope of reaching the finals, but Nixon said Vaughan would not be rushed back.
"I actually had a bat with Michael in centre wicket practice a few days ago and his hamstring wasn't quite up to scratch," Nixon said.
"He struggled running, he is still having a lot of rehab, doing a lot of swimming pool work, and having a bit of acupuncture.
"I don't think Vaughany will be taking much part, I really don't, sadly. It is too sore at the moment."
Speaking to the media last Sunday, Vaughan admitted he was still feeling the injury whenever he tried to run.
Having never had a hamstring injury before, he was unsure how long he would be sidelined for, with England crying out for his leadership.
The lingering injury is also a major blow to Vaughan's preparation for the World Cup, which is just over a month away.
It occurred in just his second game back from a long layoff due to knee surgery.
England's next match is against Australia on Friday.
The English are hopeful opening bowlers Jon Lewis (ankle) and James Anderson (back) will be available to face the Australians, but the pair will be monitored over the next few days.