2010 US Open champion McDowell was one shot on the wrong side of the cut line after a 74 which which included four bogeys.
Graeme McDowell says he is frustrated with his game after carding a second-round 74 in the Irish Open
The Portrush man bemoaned the "slow" pace of the greens but acknowledged that he is currently struggling with some swing issues.
"I'm a little off technically. I'm not quite on with my golf swing," he added.
After his round, McDowell was hoping that he would squeeze into the weekend action but he will remain at Carton House to get in some practice ahead of next week's French Open.
Three-time major winner Harrington blamed "poor wedge play" for his exit after a four-bogey 74 while 2011 Open champion Darren Clarke's frustrations continued with a second straight 75.
Galgorm touring professional Gareth Shaw is the second best-placed Irish player after a 68 left him on three under with Alan Dunbar (72), Simon Thornton (73) and club professional Damien Mooney (68) all a further shot back.
Mooney's 68 was helped by a hole-in-one at the seventh as he made an Irish Open cut for only the second time in 20 years of playing the event.
Michael Hoey, one off the lead after an opening 67, lost ground as a 76 dropped him back to one under.
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