It has hired Melbourne firm Melbcon for $9.4 million building works at Beechworth Secondary College.

The Border Mail has been told of fallout between Melbourne workers and others on site last week over concerns about travelling from the COVID-19 hotspot.

Melbcon's construction manager Shannon Synnott said: "It's a storm in a teacup, nothing to comment on."

He said the workers from Melbourne were permitted to be at the site and were following stage 4 requirements when they returned to the capital.

Beechworth Secondary College principal Patricia Broom said the workers were working in a compound fenced off from students and staff and she was unaware of any incidents.

The department declined to say if it was aware of the incident or if it would seek out North East builders in future.

All contractors from Melbourne working on the Beechworth Secondary College building site have permitted workers permits, in line with current requirements.

Melbcon is believed to have sourced 80 per cent of labour hire and materials from the North East.

An Education Department representative said that contractors were required to limit the number of sites they work across and a COVID-Safe plan was in place.

Wodonga MPs Bill Tilley and Tim Quilty criticised the use of Melbourne workers.

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"It's another example of how money is taken from the regions, spent in Melbourne, to deliver something back to the region that we could have done ourselves," Mr Quilty said.

"There are many excellent building firms in northern Victoria who would be more than capable of doing great work on this project.

"Using northern Victoria workers ensures there is minimal risk of virus transmission as well as giving a welcome boost to the local economy which, in the current climate, would be very welcomed."

Mr Tilley described it as a "classic case of the confusion and frustration that is killing our community".

"It's the lazy policy of this Victorian Labor Government that allows these workers to travel from Melbourne because of contractual agreements when they have a history of breaking billion dollar contracts when it suits them," Mr Tilley said.

"I would fully expect that there are local tradies who are more than capable of doing this work, particularly given the current restrictions that prevent many of them from crossing the Border."

One beneficiary of the Melbourne workers has been Beechworth Motor Inn owner Rob Ransom who has been accommodating them, at a time when all other bookings have collapsed because of restrictions.

"There's a lot of Melbourne companies coming up and doing jobs around the site, which seems a bit strange considering what's happening in Melbourne," Mr Ransom said.

The school work, which includes a new science resource centre, is due to be completed for the 2021 school year.