Miller was one of three riders pulled from the test alongside Pramac teammate Toprak Razgatlioglu and factory Yamaha rider Alex Rins.
On Tuesday, Fabio Quartararo crashed his YZR-M1. After being evaluated, the Frenchman returned to the track at which point the issue reared its head.
A second crash ultimately ruled Quartararo out of the test, having suffered a broken finger.
On Wednesday, knowing they had an engine issue, Yamaha elected to park its bikes.
“Basically, after yesterday, Fabio had to stop on track and we checked what was the problem,” said Yamaha technical director Massimo Bartolini.
“We didn’t find the solution. We have an idea, but considering the safety of our riders and the other riders, we decided before to come back off the track to really understand what was the problem, what we should do to be safer.
“We decided for today (Wednesday) not to run and to keep checking and try to figure out for tomorrow (Thursday) and hopefully we find a good solution for this evening so we can run tomorrow.”
Asked if the engine issues would preclude them from taking part in the third day of testing, Bartolini offered some optimism.
“I hope we find a solution and the test is not over and as I say, we still have to check,” he explained.
“We are in contact with Japan. Italy just woke up, so we will get in contact with them as well.
“What caused it is what we are trying to figure out, because if you have an idea what caused it you will already know if you can keep going or not. This is what we are trying to figure out.
“We also have an idea what caused it but we need confirmation from the factory.”
It’s another big blow for Yamaha after losing its leading rider Quaratararo on Tuesday to injury.
“Clearly, it would be better to not have problems and use all the track time,” said Bartolini.
“Unfortunately, our plan was to set up the bike better, get used to the bike. It’s a completely new bike for the riders.
“For us, we spent a lot of time on new parts and for the riders it’s very difficult to make lap time.
“Today was planned to fix the package and let the riders ride, unfortunately, they can’t.”
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