The Chino Valley Unified School District started the sessions after realizing the schools had fallen short of the state-ordered minimum class times.
It could cost the school district $5 million in penalties.
California's State Board of Education voted unanimously in Sacramento to flunk the plan to use the July sessions at Rolling Ridge Elementary School and Dickson Elementary School to make up the class time.
The board "isn't interested in seeing the district pay the financial penalty, we just want to ensure that students get all of the instructional time they need and deserve and that the district was paid to provide," said Ted Mitchell, board president.
Interim district Superintendent Wayne Joseph did not immediately return phone calls Thursday seeking comment on whether the summer classes would end.
Michael Vaughn, interim principal at Rolling Ridge, said classes would be held Friday but he had no further details.
A report by the staff of the Board of Education cited lower-than-average class attendance during the summer sessions as one reason for the decision.
At Rolling Ridge, attendance ranged between 8 and 16 percent during the summer session, according to data provided by school administrators.
Grades were final by the beginning of June, so students did not face consequences for missing summer classes.
A typical summer school day at the two campuses consists of language arts, in which students read books but aren't required to do book reports; physical fitness activities; math exercises; lunch; and an hour of "enrichment" such as designing paper airplanes or researching national parks.
The district allocated $200,000 on teachers and other costs to keep the kids in school for 34 more days.
The state board staff report suggested the district could seek a legislative remedy or tack on more days to each of the following two school years to make up the lost time and avoid paying the penalty.
Assemblyman Curt Hagman, a Republican from Chino Hills, has already proposed a bill that would waive penalties against the district after it completed 10 days of makeup classes.
The Associated Press contributed to this story.