St John's College principal Rob Ferreira said just 23 of the school's 385 students were absent.
Students that are absent are still offered distance learning at home and Ferreira said they were considering each student's absence case by case.
Napier Boys' High School principal Matt Bertram said 94 per cent of students were at school, which was just below average for a Monday in winter.
The school's boarding hostel is also up and running and all students were present except for a couple who were absent for non-Covid reasons, he said.
Napier Girls' High School had 973 students out of 1042 in attendance.
Havelock North High School principal Greg Fenton was "very pleased" with the response from the school community.
Out of 1070 pupils 990 students were at school, which was in line with an average pre-Covid-19 term day when 8-10 per cent absence could be expected.
Students not in attendance are continuing distance learning through teachers posting work covered in class to the learning management system.
Fenton said this would continue for the week then the school would review.
The school appeared to have a "positive vibe" and students seemed to be happy to be back, he said.
At Kimi Ora Community School in Flaxmere principal Matt O'Dowda said 70 out of 135 students were back at school. The school lunch programme had resumed with good handwashing and hygiene practices in place.
The food is now served individually, and nothing was shared, he said.