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.
Ciara Mageean is a notable absentee from the Ireland squad for the European Team Championship meeting in Finland later this month.