The multi-million dollar project, which will include new overtaking loops at Warrenheip and Millbrook and rebuilt stations at Wendouree and Ballan, will be ready by the end of 2019, the state government said.

It is believed there were concerns about a date listed in this year's capital expenditure budget papers, on page 160 in paper four, which listed a "completion date" for stage one of the project as the fourth quarter of the 2019-20 financial year, six months months later than what is on the Regional Rail Revival website.

Stage two is listed as being complete by the fourth quarter of 2022-23.

However, a government spokesperson said the concerns were "scaremongering" from the state opposition.

"The Ballarat Line Upgrade and Shepparton Line Upgrade are not delayed," they said.

Regional Rail Revival director Mark Havryluk said "huge progress" had been made.

"Construction is due to finish by the end of 2019," he said in a statement.

The state opposition's public transport spokesperson, David Davis, was phoned for comment.

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