Schools effectively countered the missionary effect with aggressive recruiting, said David Buhler, the state commissioner for higher education, in a statement.
"They have undertaken significant and targeted efforts to recruit new students and encourage others to remain enrolled until they leave for missionary service," he said. "It is clear that these efforts have been successful."
LDS men can now leave for missions at age 18, right after high school, rather than age 19, and women can go at 19 instead of age 21. All able Mormon men are generally expected to complete a mission, and women have signed up in droves since the age change.
So far, the number of college men is down more than women 2.75 percent compared to 1.56 percent.
Though the bulk of Weber State's drop was due to the economy, provost Mike Vaughn said the missionary change also contributed. "We had two effects happen same time," he said.
At Dixie State, now in its first year with university status, spokesman Steve Johnson said the drop was in line with expectations, and recruiting outside Utah helped soften the blow the number of out-of-state and international students went up by 31 percent this year.
SUU officials, meanwhile, said their enrollment decline was less than expected, and they're planning to switch future recruiting efforts to returned missionaries rather than just high school students.
But two schools, Salt Lake Community College and Snow College, posted gains of 3.4 percent and .13 percent respectively.
For SLCC, that increase is driven by part-time students in a separate count of full-time equivalent students, their numbers dipped about 4 percent.
"From term to term, you might see a segment of students who really want to take classes in the evening, maybe they're a little apprehensive about where they're going to be in six months," said Joseph Diaz, director of institutional research.
USHE spokeswoman Pam Silberman also pointed to the growing number of concurrent enrollment students taking courses at SLCC while in high school.
Snow, a junior college made up of about 90 percent LDS students, was expected to take one of the biggest hits due to missions, but an aggressive recruiting campaign helped fill seats, the college's president has said.
A total of 167,594 students are enrolled at the state's eight public schools this year and there were 171,291 last year, according to a student head count comparing the third week of 2013 classes to the same time period last year.
The losses come after years of record enrollment growth. Even with this year's drop, the number of USHE students has grown about 10 percent since 2008, and numbers could swell again in two years as students return from their missions and come back to school.