West Australian Transport Minister Dean Nalder has struggled to explain his decision to axe late night train services from Perth.

The Minister faced a barrage of questions in Parliament over the statistics being used to justify cutting the service, which the Government says costs $1.5m a year.

The cancellation was announced by the Public Transport Authority earlier this month, citing low patronage.

The Minister told Parliament he had acted on the authority's advice.

But under questioning from the Opposition, Mr Nalder had difficulty explaining how the data was calculated to reach that decision.

"The advice that I have from PTA was that the average [number of patrons] was around 80 per 1:15am and 2:15am service on the weekends and down as low as 20 and 30," he said.

That contrasted with answers he gave to reporters just 24 hours earlier when unveiling pictures of the train station planned for Perth's new Burswood Stadium.

"At this point in time, the average number of people catching the late night trains is around 20 or 30 people per train," he initially told reporters.

But later in the same media conference, he used a different figure, suggesting the number of people on a train could be more than double that number.

"The advice that I have is that it's the number that depart out of the metropolitan area, out of the CBD, at 1:15am and 2:15am," Mr Nalder said.

"They [the PTA] say there is up to 80 on a train but on average its 20 to 30 to 40 people on a train."

Minister has faith in advice from agency

Questioned further about the source and the accuracy of those figures, the Minister said he had faith in the advice from the PTA.

"I'm accepting the recommendations from the agency. They're providing the data that goes with that," he said.

"I trust the agency for providing me with an accurate set of figures."

That trust was tested in Parliament yesterday when the Opposition questioned the accuracy of the Minister's statement that the late night services were free.

"Are you aware the 1:15am service you are cancelling is not free?" asked Opposition Leader Mark McGowan.

"The advice I had from PTA is that those services are free, and I'm happy to follow that up," Mr Nalder said.

He was also quizzed on how the "average" number was calculated, and whether it included the empty trains coming into the city.

On Tuesday, he said it did not.

"The advice that I have is that it's the number that depart out of the metropolitan area, out of the CBD, at 1:15am and 2:15am," he told reporters.

The Minister's office subsequently advised that the average was calculated using both the outbound and empty inbound legs of the journey.

With the Minister urging people to vote with their feet to support the service, he was asked how many people need to travel on the train services before they would be saved.

On that question, the Minister was not sure.

"We have not set a defined number," Mr Nalder told Parliament.

The services are due to cease in April.