The government says it's working with authorities across the border on special arrangements to help Hong Kong students at mainland universities travel north for their studies.

Some students have been complaining of finding it difficult to get a place through the quota system for travelling to Guangdong for quarantine, while others have struggled to find flights as registration day for the new academic year approaches.

In response, the SAR government said Hong Kong students will be covered under compassionate quotas for crossing the border, "thereby increasing their chances to secure entry to Shenzhen or Zhuhai".

At a press conference on Tuesday, Education Secretary Christine Choi said mainland authorities will also arrange extra flights from Hong Kong to various cities – with students getting priority for booking tickets – as well as more hotel quarantine places.

Students who need assistance in getting to their mainland universities are encouraged to fill out an online form by Friday. Officials said once everything is ready, those seeking help may be given just one day's notice of their trip.

The education minister said she doesn't have an estimate as to how many students need to travel to the mainland.

"We still have to collect the data first... the exact number, we don't have that at this moment," she said.

Choi said some 18,000 Hongkongers are studying north of the border this year, but some may already have made their own way there.

She ruled out arranging charter flights for the students, saying half only need to go to Guangdong. But she said coaches could be laid on, depending on the number of students and whether the border checkpoints have enough capacity.

The minister also said the government isn't taking up a proposal by some lawmakers for students to quarantine in Hong Kong rather than across the border, because officials couldn't come to a consensus on the matter with their mainland counterparts given the two different quarantine systems in place.