Chief selector and former Ireland captain Alan Lewis said it was "irritating" that 28-year-old Morgan, who originally made his ODI debut in Irish colours, will skipper England at the World Cup which starts tomorrow.
Lewis told the Slog Sweep podcast that Ireland would be in a much stronger position had Morgan and fellow defector Boyd Rankin not decamped to play for England.
"It is a wee bit irritating to think where we could be if Eoin and Boyd were available," Lewis said.
"I look at the England set-up and over the last 10 years, three people from this little island where cricket is the fourth or fifth sport are playing for a country whose national sport is cricket," he added.
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"I wouldn't want to deprive Eoin Morgan the opportunity with the ability he has, I'd want to play at the top level, and in honesty every Irish supporter would wish him well, it's a great story, but it's a great frustration. To get our players back, that's part of the next step."
"Sorry, Ireland, but a country which has consistently imported players from around the world has no room to be critical when its better players want to play at the top level," one fan wrote on the CricInfo website.
Ireland were captained by Australian-born Trent Johnston at the 2007 World Cup while their 2015 squad boasts Brisbane-born Alex Cusack.