Mageean's coach Jerry Kiernan told BBC Sport NI that both he and the county Down woman had been informed too late about the offer of a place in the team.
The meeting takes place in Vaasa, Finland from 23-25 June.
"Ciara has already committed to running an 800m in Sligo next Wednesday (21 June)," said Kiernan.
"She ran a 1500m in Rome on Thursday and an 800m at the Northern Ireland Championships on Saturday and has other races planned over the coming period.
"She has a racing programme mapped out and also needs to find the time to do the necessary training.
"When she ran in Belfast last weekend, she was totally unaware of the European Team event and that was also the case with me until 48 hours ago."
Mageean ran the second fastest 1500m of her career in Rome as she clocked a world championship qualifying standard of 4:04.49.
With Mageean unavailable, Claire Tarplee will run the 1500m in Finland with Naas athlete Claire Mooney picked for the 800m.
While Mageean will be absent, a number of Northern Ireland athletes have been selected.
Rio Olympian Kerry O'Flaherty is picked in the 3,000m steeplechase despite being troubled by a calf injury in recent weeks.
Emma Mitchell's fine recent form earns her selection in the 3000m while Finn Valley high jumper Sommer Lecky is also picked after equalling the Irish junior record recently with a leap of 1.85m.
Amy Foster is picked for the 100m and 4x100m while Christine McMahon (400H), Ben Reynolds (110H), Adam McMullen (long jump), Dempsey McGuigan (hammer), Christian Robinson (4x100m) and Andrew Mellon (4x400m) are also selected.
In addition, Donegal-based athletes Mark English (800m) and Ann Marie McGlynn (5,000m) are picked.

The members say they'll continue as a four-piece after Zayn Malik announced he was leaving the group last week to "live like a normal 22-year-old".
His departure was followed by rumours on Twitter, Instagram and Facebook that One Direction was about to break up.
But Liam Payne thanked fans for sticking with the band and for "not thinking it's finished".
He tweeted: "I can see a lot of people thanking us for staying but your the real Heros here thanks for not thinking it's finished."
The band continued their On the Road Again tour and have been playing concerts in South Africa.
They start the European leg of the tour by playing Cardiff's Millennium Stadium on 5 and 6 June.
Zayn Malik quit the group last week after flying back to the UK, having been "signed off with stress".
It was after reports that he'd cheated on his 21-year-old fiancee, Perrie Edwards.
He told The Sun that he was "upset" for the group's fans and he said there was no bad blood between him and his former bandmates, who he said had been "really supportive".
It's thought he's working on a solo album with producer Naughty Boy, who's worked on tracks for Emeli Sande, Cheryl Cole and Leona Lewis.
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The 27-year-old has made 73 appearances for Blues since joining in 2013 but spent the past 18 months out on loan.
Last season, the once-capped Scotland international helped Hibernian win promotion to the Scottish Premiership, scoring three goals in 32 games.
"To get him for Luton is a real coup for the football club," Hatters boss Nathan Jones told the club website.
"We lost a wonderful player in Cameron McGeehan [to Barnsley] and what he does is difficult to replace, but we have brought in a different Championship-quality player and we are delighted."
Find all the latest football transfers on our dedicated page.
Ciara Mageean is a notable absentee from the Ireland squad for the European Team Championship meeting in Finland later this month.
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One Direction is not on the verge of splitting up, despite rumours started on social media.
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League Two side Luton Town have signed midfielder Andrew Shinnie on a season-long loan from Birmingham City.