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The ICC, cricket's global governing body, said the experienced Harper had been omitted after an expert panel concluded his "general performance" did not merit selection for the event.
However, in a statement issued from their Dubai headquarters on Tuesday, the ICC "categorically stated" Harper had not been dropped because of his controversial role during the fourth Test between South Africa and England in Johannesburg in January.
Harper stunned England by deciding to give South Africa captain Graeme Smith not out caught behind on review in an innings where the opening batsman went on to make a century that led the Proteas to a series-levelling victory.
The subsequent controversy saw Harper and broadcasters accuse one another of making mistakes in ensuring the technology needed to operate the decision review system was working properly.
It led the ICC to set up a review, still ongoing, with former West Indies captain Clive Lloyd at the helm, into the incident.
Explaining Harper's absence from the World Twenty20, which starts next month with Pakistan the defending champions, the ICC said: "This decision was taken by the selection panel for a number of general performance reasons.
"It must be categorically stated, however, that none of these reasons is related to his role as third umpire in the fourth Test between South Africa and England in Johannesburg earlier this year."
A 13-strong umpires' list features all 10 of Harper's colleagues on the elite panel, including fellow Australian Simon Taufel who on Wednesday was standing in his 150th one-day international, between the West Indies and Zimbabwe in St Vincent.
They are joined by South Africa's Marais Erasmus, Australia's Rod Tucker and India's Shavir Tarapore.
The selection panel that chose the umpires and match referees for the World Twenty20 was made up of ICC general manager - cricket Dave Richardson, the former South Africa wicket-keeper, ICC chief match referee Ranjan Madugalle of Sri Lanka, former England batsman, coach and first-class umpire turned broadcaster David Lloyd and Srinivasaraghavan Venkataraghavan, the ex-India spinner and former elite panel umpire.
Umpires for World Twenty20
Billy Bowden (NZL), Aleem Dar (PAK), Steve Davis (AUS), Billy Doctrove (WIS), Ian Gould (ENG), Tony Hill (NZL), Rudi Koertzen (RSA), Asoka de Silva (SRI), Simon Taufel (AUS), Asad Rauf (PAK), Marais Erasmus (RSA), Shavir Tarapore (IND) and Rod Tucker (AUS)
Match referees for World Twenty20: Ranjan Madugalle (SRI), Alan Hurst (AUS) and Jeff Crowe (NZL)
