Downton launched a scathing attack on former England batsman Pietersen during an interview with BBC Radio's Test Match Special on Thursday.
The ECB chief said Pietersen appeared "disinterested" and "distracted" in the fifth Test in Sydney, and that he was unable to find anyone within the England set-up who wanted the controversial 33-year-old to remain in the team.
England's thrashing in the Test series in Australia was the beginning of the end for Pietersen, who was reported to have strained relations with several members of the squad and was eventually axed in February with Downton overseeing the decision.
"The suggestion that I was uninterested during the winter Ashes series against Australia is wholly untrue," Pietersen said in a statement.
"Although I was having injections in my knee, which inhibited my mobility and thus my ability to field close to the wicket, I was fully motivated to play for England and whilst I accept that the series as a whole fell well below my own personal standards, I finished the series as the top scorer.
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