Both of Eau Claire's public high schools failed to meet part of the standards in the federal government's "No Child Left Behind" Act.
At North, reading scores among Asian students and math scores among disabled students didn't meet a raised threshold.
At Memorial, students with disabilities scored below national standards in reading.
Schools don't get penalized until they fail the same area two years in a row, but district officials are still frustrated at being labeled as "failing."
"In fact, we're looking at a very small number of kids and we're looking at kids who are in specialized programs to help meet their needs," says Tony Beardsley, the director of pupil services.
On a visit to Eau Claire Monday, Jessica Doyle said the standards have a good intent, but they fall short in illustrating students' progress.
The first lady was visiting Robbins Elementary School as a kick-off for this year's "Read On, Wisconsin" program.