Scaffolding is now covering the heritage-listed structure after the state government committed to make the tower weatherproof and structurally sound.

School principal Peter Auchettl said the tower had been leaking during strong weather and the works followed an earlier refurbishment of the school's roof.

"It's taken 12 months for the engineers in Melbourne to figure out how best to tackle it," Mr Auchettl said.

It's unknown exactly when the bell tower was built, but Mr Auchettl believed it was likely relocated from the Warrnambool Agriculture College to the Jamison Street frontage sometime between 1911 and 1915.

The school rosters year three-four students to ring the bell twice a day, once in the morning and once to end the school day.

"The kids just love it, they love the opportunity," Mr Auchettl said.

Mr Auchettl said he had climbed the bell tower about half a dozen times in the past to repair the rope-and-pulley system that rings the bell.

The tower is among the tallest structures in Warrnambool. "There's amazing views," Mr Auchettl said.

The building had terracotta roof tiles replaced for the start of the 2019 school year.

The Department of Education and Training said the bell tower works could extend until May.

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