Trains will now depart Wendouree or Southern Cross roughly every 20 minutes during peak hours and every 40 minutes in off-peak times.

However, the total travel time for each trip has increased with peak services in both directions now stopping at all stations except Melton, Cobblebank, Caroline Springs and Ardeer.

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Public Transport Users Association Ballarat branch convenor Ben Lever said most Ballarat services lost between four and nine minutes per journey, but the difference was counteracted by reductions in wait times.

"Broadly, the new timetable delivers on what the new infrastructure of the Ballarat Line Upgrade allows, which is more frequent services, both during the peaks and throughout the rest of the day," he said.

"This is a huge benefit, because it means passengers will generally have less time to wait for their next train, which ultimately gets them home more quickly."

With the increased frequency, a missed train will now result in only a 20 or 40-minute wait rather than the previous 40 to 60-minute wait.

Mr Lever said daily peak commuters will be the ones to feel disadvantaged as their usual journey time increases and they do not benefit from the greater service frequency.

"This is unfortunately a consequence of the need to stop at more suburban stations between Melton and Sunshine, since the Ballarat line has to serve both regional and metro passengers, and their populations keep growing year after year," he said.

"It's long overdue for Melbourne's west to get a proper Metro service, so we need the line to Melton to be electrified, and for extra bypass tracks to be built between Melton and Sunshine so that Ballarat trains can have a nice clean run through this section."

However, Ballarat-based commuter Joelene Waters said she was disappointed with the new timetable.

After moving to Ballarat with her partner and newborn with the intention to commute into Melbourne, Ms Waters said the last thing she expected was for travel times to increase following the Ballarat Line Upgrade.

"We moved to Ballarat with a newborn baby because we heard there would be improvements to the Ballarat line and we've dealt with a significant number of delays and train replacement coach services since moving here," she said.

"Both of us do roles that require us to do full days so we dealt with the commute knowing there was a light at the end of the tunnel.

"I understand you need to improve services along the line but I thought there would be some consideration given to people living in Ballarat. It was definitely news to us when we opened up the timetable."

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Rail advocate Nick Beale said weekday services had increased by 100 per cent since 2010.

"In terms of history, in the last 25 years there has been a 300 per cent increase in the number of services to and from Melbourne. In that time the population of Ballarat has grown by about 40 per cent," he said.

"The main negative of the new timetable is that the average journey into Melbourne time has increased by 8 minutes and on the return trip by 4 minutes.

"Gone are the 2010 days when the one express train in and the one express train out had a 64 minute journey.

"The truth is there is no express service in and out of Melbourne. All the commuter morning and evening services are between 76 and 80 minutes."

Member for Wendouree Juliana Addison said the increased travel time was a symptom of the growth in Melbourne's outer west.

"The reason that the duration of our train trips have been extended is because we've added train stations at Cobblebank as well as more stops at Deer Park. This is very much about making sure that the Ballarat Line Upgrade benefits the greatest number of people who live in the western corridor," she said.

"While it is an extra few minutes for Ballarat passengers, I understand that, what I am really happy about is there'll be less time waiting on a platform for a train to arrive and a much greater chance of getting a seat."

Ms Addison said the Ballarat Line Upgrade was not the end of improvement to the service, with planning money issued for the electrification of the line to Melton.

"My understanding is that there has been some planning money put to the electrification to Melton, talked about as an election commitment, and that planning work is underway," she said.

"This is not the end of the line for the Ballarat line, it is certainly something that we are going to continue to invest in."

A Department of Transport spokesperson said minor changes in travel times were caused by altered stopping patterns on some services.

"From Monday, Ballarat line passengers will have a train every 20 minutes in peak for the first time giving them more options than ever before," the spokesperson said.

"We're also making it easier for passengers to stagger their journeys and work flexible hours, with a train every 40 minutes off peak and 80 new services a week stopping at stations in Ballarat."

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