Education minister Christine Choi says the authorities have formed an inspection task force to probe suspected "shell schools" for students from outside Hong Kong.
At least two private schools in the city have had their operations stopped or suspended in recent weeks amid such concerns.
They have denied partnering with non-local education centres to let students sit public exams in the SAR as locals, enabling them to apply for public universities as Hong Kong students.
Choi said the government has zero tolerance for shell schools as they are not registered.
She said the task force, which includes education officials and people with experience of managing schools, will go through data such as student numbers and attendance rates, as well as teacher registration records.
Officials will aim to complete the first phase of their probe in September, looking at "high risk" schools that have had operational, financial or enrolment issues.
"We assess the high risk schools by checking if the schools are facing difficulties admitting students, and we would also look at information through the media and on the internet. Officials will also do spot checks in different districts," Choi said in an RTHK interview.
"If we find clear evidence of violations, we would revoke their registration. For suspected cases, we will give schools ample time to explain themselves and provide evidence to us."
The minister said in the second phase of the investigation in October, officials will also look at schools that have had difficulty in admitting enough students.
Choi said if officials find suspected violations and fraudulent activities, her bureau will forward the cases to law enforcement agencies on both sides of the border, noting that the bureau has an information sharing mechanism with mainland counterparts.
She added that the bureau is seeking to compile a list of private schools which promise to operate legally, for parents' reference.
Meanwhile, the education chief dismissed suggestions that hundreds of thousands of mainland students who were born in Hong Kong will rush to attend universities in the SAR in the coming years.
Nonetheless, she stressed that such students are also Hongkongers and that they have the freedom to study in the SAR if they wish.