Since July 2013, V/Line has been building a new, raised bridge section over the roadway to prevent large vehicles hitting the bridge.

A V/Line spokesman said the bridge was being replaced and raised.

“What we are doing is constructing a new bridge,” the spokesman said.

“Our main purpose is to raise the height to stop vehicles coming into contact with the bridge.”

The spokesman said the bridge was the site of several accidents where road vehicles had struck it and caused severe disruption to V/Line trains.

"Each strike prompts the need for us to inspect the bridge before we are allowed to run trains over it again,” he said.

Some works on the $1.8 million project were done during Regional Rail Link shutdowns last year.

V/Line is using this summer's longer absence of trains to finish the work.

The spokesman said that aside from preventing train delays, another potential benefit was that vehicles previously not able to fit under the bridge would now be able to.

But he said they also had problems with backhoes.

The new bridge would "not stop locals who attempt to drive under the bridge with backhoes in trailers".

“We are investigating the installation of flashing sign technology that will detect oversized vehicles and flash a warning before the motorist attempts to drive under the bridge,” the spokesman said.

He said Skewes Bridge had posed the biggest problem with oversized vehicles on the Bendigo line due to its proximity to the highway and Castlemaine.

The section of bridge being replaced was made of steel beams with timber decking and was not considered to have any heritage values, he said.

The bridge is scheduled to re-open to trains on 27 January.