The McLaren driver went off at Spoon early in the Friday afternoon session at Suzuka, sidelining him after just eight laps.
He will be forced to revert to chassis #1 for the remainder of the weekend.
"On the entry I put a wheel on the AstroTurf and lost the back end," said Perez.
"There is not much room so I went straight into the wall.
"Unfortunately I think we lost quite a lot of work today, especially for the high-fuel run and to feel how the option tyre was performing.
"But I'm looking forward to tomorrow, I'm feeling comfortable with the car so I think we can recover."
Perez confirmed that he was unhurt in the crash and that a delay in exiting his McLaren was not due to any discomfort.
"The marshals didn't want me to get out of the car, they were waiting, which was the main reason," he said.
His team-mate Jenson Button said the crashes for Perez and other drivers on Friday showed what set Suzuka apart from other F1 tracks.
"It's unforgiving," said Button. "I obviously don't like seeing accidents like Checo's but you can see this circuit does not forgive and you have to give it a lot of respect."