The head of Metrolinx says it's "not acceptable" that as many as 12 per cent of Presto card readers on TTC buses don't work, and said the agency aims for 99 per cent reliability across the system.

Metrolinx, which runs the Presto program, conducted a field audit over the last few days and found that 94.5 per cent of readers on streetcars are working, while 88 per cent of readers on buses are working.

"Obviously, that's not acceptable to us," Metrolinx president and CEO Bruce McCuaig told CBC's Metro Morning on Friday.

The agency is working with TTC staff to get the readers back online, and then will determine what has caused the outages "so it doesn't happen again," he said.

A number of factors could be contributing to the outages, according to McCuaig, including software or hardware issues, or network connectivity problems.

There are about 12,000 readers across the region that are all connected wirelessly.

There could also be an issue with the front-line maintenance of the readers that is handled by TTC staff, McCuaig said.

"We don't know yet which combination of those factors may be contributing to the device reliability issue," he said. "But we will get to the bottom of it and we will correct it."

Presto to be fully implemented in 2017

The Presto fare system is being phased in across the TTC in stages, a process that is expected to be completed by the middle of 2017. During this transition period, some customers have gone public with complaints, including payment not registering, or multiple payments being taken off a card for a single trip.

According to McCuaig, the system is adding between 10,000 and 20,000 new customers each week, and there are about 750,000 "taps" of Presto cards on the TTC each week.

In August, the TTC said readers had been installed on nearly half of the agency's 1,900 buses.

As for streetcars, McCuaig said the original plan was to deploy the readers only on the new streetcars, but because delivery from manufacturer Bombardier has been delayed, Metrolinx has had to include the older streetcars in the program.

"That's a unique challenge because first of all the age and the quality of the electronics and power on those streetcars make them a particularly unique environment in which to operate basically a computer system," McCuaig said.

Metrolinx is also working to make Presto cards available at TTC stations, he said. So far, the cards are available at seven Gateway outlets at various stations, and "many, many more" will be added in the coming weeks and months.

Meanwhile, McCuaig urged riders to report any problems in the system so they can be addressed. You just can't do that online for the next four days. The website is down for maintenance.