The number of fare paying customers using public transport in Perth has declined for the second straight year, but overall patronage is up slightly.

Fare paying passengers on the Transperth network dropped 1.5 per cent in 2014-15, according to the Public Transport Authority's annual report, following a 2.6 per cent decrease the previous year.

Overall patronage was up by 0.8 per cent, driven largely by people travelling for free on special events days such as Anzac Day or The Giants performance, or due to concessions for seniors and pensioners.

In the report, the PTA admitted the 2014-15 patronage results were "unfavourable" but said total boardings were still up by nearly 10 per cent over five years.

Managing director Mark Burgess said there were a number of factors causing weakening patronage demand, while two major rail shutdowns as part of Perth City Link works also had an impact on the figures

"One outcome has been a drop in the number of people working in the CBD ... thus weakening Transperth Trains' core market base: commuters," he wrote in the report.

"Another has been a reduced population growth rate after several years of unparalleled increases, which also shows up as a lower level of demand for our services."

But Labor disputed the notion a declining number of workers in Perth's CBD was a factor in the figures and said people were voting with their feet.

"Congestion on the rail and bus network is an issue and people are getting less satisfied with their ability to get a seat, in particular on a train," Opposition transport spokeswoman Rita Saffioti said.

"Increased fares is also putting a lot of people off because we've seen a consistent increase in fares year-on-year."

Transperth's system generated revenue of $223 million, up by 3.4 per cent, with fare revenue making up $198 million of that total.

In the regions, patronage on the Transwa train network fell 0.43 per cent, with passenger numbers on the Australind train linking Perth to Bunbury down nearly five per cent.

Passenger numbers on regional coaches also fell by nearly 5 per cent.