Maguire made his debut in the qualifier against Moldova and was likely to an option to Martin O'Neill after some impressive club form with Preston North End, including goals against Fulham and Brentford.
Independent.ie report that Maguire has suffered a "serious hamstring injury" which will require surgery and could keep him out of action for three months.
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Maguire has suffered an injury similar to Greg Cunningham, one of a host of defenders now unavailable to Alex Neil, and will need an operation. It's said that the 23-year-old is believed to have sustained a hamstring injury in the interim.
The news comes as a blow ahead of next Saturday's first leg in Copenhagen, with Jonathan Walters also confirmed to be ruled out during last week's squad announcement.
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This is gutting news for the ex Cork City man..
Manager O'Neill is hopeful that Nottingham Forrest striker Murphy returns to full fitness after missing the side's last two games when they take on QPR this afternoon.
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With a week to go until Ireland face Denmark in Copenhagen in the first of two crucial play-off games for the World Cup, they have been handed some bad news.