The majority of Melbourne bus passengers wait at least 20 minutes between bus services - and then have to wait for trains, too.
Wide variations between weekday and weekend schedules can also leave passengers waiting 40 minutes for a train.
Auditor-General John Doyle has called for more harmony between Victoria's various train, tram and bus schedules.
"Many of Melbourne's bus routes currently have long wait times, indirect routes and do not operate on schedules designed to harmonise well with the rail network or other bus routes," Mr Doyle said.
Public Transport Victoria (PTV) data showed 80 per cent of bus services had an average wait of 20 minutes or more between services.
About 39 per cent of bus services took more than 10 minutes to connect with key train services.
Mr Doyle also said Victoria's $2.7 billion public transport contracts lacked any way to make sure trains, trams and buses were co-ordinated.
He said future contracts should include incentives for system-wide co-ordination to make sure transport companies complied.
But Mr Doyle did praise the introduction of PTV as a key development driving better planning and co-ordination.
Public Transport Minister Terry Mulder said PTV's introduction was one of the reasons trains, trams and buses were running more frequently.
"They are clearly focused on customers, they are clearly focused on getting the best value for dollar in the public transport arena," Mr Mulder said.
But Public Transport Users Association president Tony Morton said PTV had a difficult job making bus timetables fit better with trains and trams.
"A lot of the existing bus contracts don't necessarily have the flexibility to allow network operators to work with the bus operators to actually make changes that are warranted," Mr Morton told AAP.
Mr Doyle's report, tabled in parliament on Wednesday, found weekend waits for trains could be up to 40 minutes, which was exacerbated when passengers also needed a bus connection.
A review of timetables in two areas found they "were barely better than if they had been written with no consideration" of connecting to other services.
Mr Morton said more direct and more frequent bus services were one key to encouraging people to take public transport instead of driving.