A secondary school in Tsuen Wan that recently suspended its pupils over a flag raising ceremony said on Monday it's launching an independent inquiry into the matter.

Fourteen students at St Francis Xavier's School were suspended for three days this month, for allegedly "disrespecting the national anthem and emblem".

In a letter to parents posted on Facebook, the school said it expects the probe will take about three months.

"The independent inquiry will submit a fair and just report to [the school's] Incorporated Management Committee, giving an account to teachers and pupils, parents and public, and winning back everyone's confidence in the school," said the school's supervisor, Reverend John Chong.

He called on parents to allow the school to return to normal operations, teachers to focus on education, and pupils to study happily.

Some critics, including education sector lawmaker Chu Kwok-keung, had noted that class suspension is quite a serious penalty, and schools should weigh how punishment can help pupils recognise their mistakes.