For the first time, New York City students are using an online system to submit applications for middle and high school admissions as they race to meet the Dec. 3 deadline. But the system has arrived late in the process and is creating new headaches, according to some guidance counselors.

The new website replaces the old process: students filled out paper applications that ranked their school choices and turned the paperwork into their guidance counselors, who would enter the information into a central system.

Students can still fill out paper applications, according to the city’s education department. But now, parents can go directly on to its MySchools site and create an account, which their children then use to rank their top choices for middle or high school. The website can also be used to apply for gifted and talented programs.

But a bumpy rollout, including glitches in the system and a poorly designed portal for schools, is making it harder, counselors say, to help students navigate the process or select schools for next year.

“A school that just kind of wants to wipe their hands clean of responsibility — this would do it,” said one guidance counselor at a Queens middle school who wished to remain anonymous.

How widespread the portal problems are remains unclear, but a department of education spokesman did acknowledge it has received complaints — for example that the system is too slow for users.

Education officials said the department decided to make the change as a previous contract was expiring, which provided a chance to modernize the application system.

The new website lets families search schools that match certain preferences, like academic programs, sports or other activities, accessibility, and proximity to particular subway lines. And people who spoke to Chalkbeat said they’ve heard positive feedback about the portal for parents — that it’s easy to use for people who are already familiar with computers.

But the portal — available in ten different languages — could still present challenges for parents who can’t read, lack access to a computer or are not familiar with such technology. And the separate portal for schools was described as basic and rife with delays. One counselor compared it to the old operating system MS-DOS.

The department announced its plan, part of a long-awaited diversity initiative, to switch to an online system in June 2017 and said the transition would happen in the fall of 2018. Officials notified superintendents about the transition in April and told principals in June.

But education officials did not host in-person and webinar trainings for guidance counselors until September and October. This is also when families received letters notifying them about the changes, although education department officials say those families that attended summer high school events were also notified of the transition from paper to the MySchools portal.

The Queens counselor said her school reviewed the old process with seventh graders in the spring so that they would be ready as eighth graders to apply for high schools of their choice. She heard changes were coming but was not informed about when they would go into effect or what the system would look like until September.

“If they wanted to do this, they probably should have started a little earlier,” said another guidance counselor at a Brooklyn middle school.

One issue both counselors raised is they can no longer readily identify which students have yet to fill out applications. Under the old system, while cumbersome, counselors could check different classes and see who was missing from the list. The old system, the Queens guidance counselor said, made checking up on every student in her caseload easy. When she found students who hadn’t applied, she could quickly turn to “hunting them down, calling them and talking to them.”

The responsibility for making sure students were making progress was “on my shoulders,” she said. “I can’t do that anymore.”

The Brooklyn counselor said about 50 percent of students have still not filled out their applications at her school — which she only discovered after education officials sent the school a letter just a couple of weeks ago.

The education department could not immediately answer a follow-up question about how many students have filled out their applications to date compared to this time last year.

In the past, because counselors would receive sheets with their students’ school choices, it was easier to advise them on whether selections matched a student’s performance or chances of being accepted. This might prevent an adult from unduly discouraging a student from considering schools that some might judge out of reach. Under the new system, families can make their choices without a counselor actively involved in the process. But students who genuinely need guidance, encouragement or just logistical help may now miss out on such support or trouble-shooting, which could end up disadvantaging students who need assistance the most.

“A parent that does not communicate with us or thinks they have it under control, or a parent that is just putting it off until the last minute — we’re not going to be able to do much,” the Queens counselor said.

Raina Narita, a high school placement associate for Breakthrough New York, a nonprofit that helps low-income students with educational support like tutoring and navigating the admissions process, said that counselors may be right that the system is likely to be a challenge for parents who have little to no experience with computers, or lack access to them at all.

Parents who don’t have such access can still use the paper process or go to a Family Welcome Center, but not all parents may be aware of such options. Narita and both counselors say they have spoken to several parents who never received the letter that instructs them on how to create a MySchools account.

Officials said they have worked with the developer to address issues with the system, including problems with slow speeds that popped up last week and are keeping families apprised of changes and have received “positive feedback” about these efforts.

“We’ve made our application process easier and simpler by bringing it online with MySchools, and families no longer have to mail applications or complete paper applications at school,” said Doug Cohen, spokesman for the Department of Education.