The de Blasio administration is close to its goal of offering a pre-kindergarten seat to every four-year-old in New York City. Making sure that most of those seats are full every day is another challenge.

On that front, families did well last school year: Nine in 10 students showed up on an average day across the city’s nearly 1,700 schools and community organizations offering pre-K, department officials said last week, though that number is lower than the city’s overall school attendance rate. With the pre-K population about to swell for the second year, it’s a number city officials say they are keeping an eye on.

“We really need to make sure that parents understand that you don’t take off because he has the sniffles or because it’s Monday and he didn’t go to bed early,” Chancellor Carmen Fariña said last week on “Inside City Hall.”

Fariña’s comments reflect a common concern among early education advocates in New York City and nationwide. Students, especially those living in poverty, are more likely to be chronically absent in pre-kindergarten and kindergarten than at other points in elementary and middle school, a phenomenon that experts say can stem from parents’ instincts about their children’s health and transportation challenges.

Hedy Chang, director of the nonprofit Attendance Works and the author of a recent policy paper on early education absences, said another hurdle is the perception that absences matter less for younger students than it does for older students.

City officials expect more than 60,000 children to enroll in a full-day pre-K program this year — triple the number in those programs two years ago. But for students to reap the academic benefits of pre-K, attendance is key, Chang said, and research has linked absences at early ages to higher dropout rates and lower test scores in later grades.

“There’s that perception that school doesn’t really matter that much in kindergarten and pre-kindergarten,” Chang said.

A classroom full of four-year-olds can be a hotbed for contagions, but parents keeping children with mild illnesses away from school is unlikely to reduce the spread of germs, according to Terry Marx, a pediatrician and the assistant medical director at Children’s Aid Society. More effective, she said, is teaching children good health habits, like washing their hands.

Marx repeated that message to a group of about 40 pre-K educators during a training session at Children’s Aid’s Harlem offices last week.

“There are a lot of programs and a lot of old-school ways of thinking, where the kid sniffled or sneezed and they were out the door,” said Marx, a pediatrician. “We don’t operate that way.”

“That’s not the goal of school,” Marx said. “We want to keep them in school.”

What’s the magic number for reasonable absences? Moria Cappio, vice president of early childhood programs at Children’s Aid, said that her 14 pre-K centers are audited annually by the city’s Department of Health and Mental Hygiene, which requires that the centers have an average monthly attendance rate of at least 85 percent. Cappio said she was looking beyond her average daily attendance number, though.

“It’s not really telling the true story,” said Cappio. “You could have four kids that miss three days a week, every week, and your center’s average will be above 85 percent. But it’s those group of kids you should be really worried about because something’s going on in their little life that’s making them chronically absent.”

Children’s Aid began closely monitoring such chronic absenteeism last year, and discovered that more than half of its enrollees were absent at least two days a month. Those students showed weaker language, math, social and motor skills than students with strong attendance — data points that Cappio shows to parents to stress the importance of coming to school.

City officials said the overall chronic absenteeism rate in city schools last year was 19 percent, although they did not provide that number for individual grades. Sophia Pappas, who oversees the early learning operation at the education department, said the chronic absenteeism rate for pre-K was similar to the rate for kindergarten, which in 2013 was 27 percent.

Pappas said her office has hired more social workers to work with pre-K sites, and that the department is also now sponsoring training for program administrators focused on working with families.

“There may be programs here and there that need help from us, but that’s why we have a lot of people on our team to develop strategies to support them,” Pappas said.

If families get in the habit of ensuring their children’s daily attendance at a pre-K program, Fariña said, it will only benefit students.

“Getting to school every day as you move up the grades is more and more important,” Fariña said.