The 34-year-old former England captain, who resigned during his side's recent series defeat against South Africa, will not be in the Test squad, due to be announced on Monday, because of his poor batting form for Yorkshire recently.
Vaughan will take a three-month break from international cricket in an attempt to rediscover his form in time for next year's Ashes series.
"Michael has not been selected for the tour of India because his place in the Test squad cannot be justified based on recent form," Miller said.
"Our view is that it will be to England's benefit if he takes a break from international cricket in the period leading up to Christmas and spends time working on his game."
The ECB have discussed the situation at length with Vaughan and come to a mutually agreeable solution.
The hope is that Vaughan, this month awarded a central contract, will be able to return to his best - and to the England team - either in the Caribbean next spring or in time for the 2009 Ashes.
"We have discussed the situation with Michael," Miller added. "He fully understands the reasons for the selectors' decision and has made clear to us that he is fully committed to winning back his place in the England Test side.
"Like all centrally contracted players, Michael will be given a clear programme over the next six months which will include training and match practice over the winter period.
"With a busy period of international cricket on the horizon, we would like to stress that he remains very much part of our plans over the coming year."