Fecal bacteria has been found in Perth's new $440 million Elizabeth Quay inlet, after concerns were raised over the water quality for a swimming event scheduled for the weekend.

The AustralianSuper corporate triathlon series 2016 was due to take place this Sunday.

However organisers say the 400-metre swim leg has been replaced with a running section, after they were informed by the Metropolitan Redevelopment Authority (MRA) that the water quality was not of a satisfactory level for swimming.

MRA chief executive Kieran Kinsella said tests have come back identifying elevated levels of pathogens, particularly fecal bacteria.

"We've done our testing regime and have come back with elevated levels of pathogens, particularly fecal coliform," he said.

"This has been deemed by the health department as unsuitable for swimming activities, and we have been advised to cut the swim leg from the triathlon planned for Sunday."

Mr Kinsella said authorities were not sure of the source of the pathogens, and that it was a "surprise to us".

He said the MRA would work with environmental consultants and taking advice of the health department to identify the source.

Mr Kinsella said the authority had conducted regular water tests since the inlet was completed in December.

The triahlon organisers said they were disappointed the swim leg had to be cancelled, but it had happened at similar events in other cities after periods of rain.

"We realise that this is not an ideal situation but we have been working hard in the last few days to create a brand new 650m run course that will hopefully not take away from your event day experience," a statement from the triathlon group said.

Testing results not public

The announcement follows enquiries by the ABC about the water quality in the quay, in relation to whether potentially harmful algal bloom was present.

Last week MRA chief executive Kieran Kinsella sent through an emailed statement saying the water was being tested by a private firm, RPS Environment and Planning.

"The testing regime is an agreed approach between the MRA, Department of Parks and Wildlife (DPAW) and the Department of Health (DoH)," the statement said.

"All reviewed results since the opening of the inlet comply with the Environmental Quality Guidelines and show no significant variation between water quality from the wider Swan River testing locations and those within the Elizabeth Quay inlet."

Tests in other parts of the Swan River have returned both low and high levels of algal bloom in recent months.

DPAW said in a statement to the ABC last week that it had been receiving monthly updates on the water quality in the quay from MRA.

"Elevated levels of cyanobacteria (blue-green algae) were detected within the Elizabeth Quay inlet between November 2015 and early January 2016, when a silt curtain was still in place and the quay was closed to the public," DPAW said.

"The silt curtain was in place to prevent debris and sediment from the site entering the river during the construction phase and while providing favourable conditions for algae growth, targeted water testing did not detect any toxins in the water and the Department of Health determined the human health risk to be minimal.

According to published results on the DPAW website, the nearby testing location near the narrows bridge shows a low level of microalgae activity.