A WA country train service which is costing $10,000 a day to run and averages just 11 passengers per trip looks likely to be scrapped, but some residents fear if it goes road fatalities will spike.

In 2013, the Barnett government backflipped on a decision to axe the train servicing the Avon Valley, running from Perth to Northam 100 kilometres east, choosing instead to fund a three-year trial which part-way through saw services increased to 28 per week.

The trial is due to finish June 30 and there are signs the service will be axed.

The cost of running the service, and another out to the Wheatbelt town of Merredin, was $7.79 million over two-and-a-half years to the end of 2015, which local member and Labor politician Darren West said made it the most heavily subsidised service in the state.

"In this environment it's really hard to sell a service that cost $10,000 a day and that only 11 people hop on each trip … the train holds 116 passengers," he said.

Mr West, who is also an Upper House member for the Agricultural Region, said he wanted to know why the services were not being used, but said buses may be a more viable service as they could stop in more towns along the route.

However the Wheatbelt region has one of the highest road fatality rates in the nation and residents have told the ABC adding more buses onto the road network was not a safe option.

Nationals leader and member for the Central Wheatbelt, Mia Davies, said Mr West's comments were "highly hypocritical" given he had supported AvonLink when it was last at risk.

Ms Davies said the service was hard fought for and if it was axed, it would not be reinstated.

"It is incumbent on every government to try and make these services work, because once they're gone that's it," she said.

"I'm not very excited about the fact that we've got a wonderful building program in the metropolitan area, which is subsidised no matter what the patronage, when we don't see that sort of investment or commitment to regional Western Australia."

Mr West said the previous government had failed to allocate funding for the project in the forward estimates, past the end of the trial.

'Numbers down because of delays'

The AvonLink travels between Perth and Northam via Toodyay, about an hour north-east of the city centre.

Shire of Toodyay chief executive Stan Scott said numbers were steadily increasing before major track work that disrupted the route for about 18 months.

"Regular users of the train on a couple of occasions ended up an hour late for work," he said.

"So people started making alternative arrangements."

Mr Scott said the service would grow and it would be a great loss to metro and country communities, as well as tourism, if it were stopped.

"Perth can't continue expanding north and south without some growth to the east," he said.

"So they will need a rail service to this part of the world eventually."

The Minister for Transport was unavailable for interview.