Mooney said he hoped the former British Prime Minister's death had been "slow and painful" in a tweet posted to his followers. The comment was deleted following intervention by Cricket Ireland chief executive Warren Deutrom.
"John Mooney has been severely reprimanded by Cricket Ireland and handed a three-match suspension following his tweet regarding the death of former British Prime Minister Margaret Thatcher," read a statement from Cricket Ireland.
"The 31-year-old was found to be in breach of clause eight of his Cricket Ireland contract which prohibits players from any public statements which it considers 'denigrates, is derogatory, or is prejudicial to the interests of cricket; or is of a nature which brings the game of cricket or Cricket Ireland into disrepute'.
"The player has accepted the Cricket Ireland decision and both he and Cricket Ireland consider the matter closed and will be making no further public comment on the issue."
Mooney, who scored the winning runs in Ireland's historic win over England at the 2011 Cricket World Cup, apologised for his comments hours after deleting the offending post, saying he accepted they "were offensive to many".
Deutrom welcomed his apology in Tuesday's statement but insisted Mooney, who made his first-class debut for Ireland in 2004, could not be excused from punishment.
"John accepted that the tweet was offensive and inappropriate. We took into consideration the fact that he issued a fulsome and swift apology and that he is genuinely remorseful for his action," said Deutrom.
"However, given the breach of his contract and nature of the tweet, we felt it appropriate that a three-match sanction be imposed. We have also severely reprimanded John and reminded him of his duties and responsibilities as a high-profile international cricketer."
The suspension rules Mooney out of the first one-day international against Pakistan in Clontarf next month, and Leinster Lightning's games against Northern Knights on May 6 and North West Warriors on May 14.
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