Makino was running inside the top 10 on the opening lap when Red Bull junior Liam Lawson suffered a spin while battling with Mugen team-mate Tomoki Nojiri for the lead.
The Dandelion driver was unable to avoid the out-of-control Mugen car ahead of him, with the contact sending his car airborne.
Makino landed on track in a near-upright position before smashing into the armco barriers adjacent to a marshal post on the other side of the track, suffering another significant hit.
RACE REPORT: Motegi Super Formula: Nojiri wins, Lawson 13th after first-lap chaos
It's understood that Makino needed assistance to exit the cockpit of his stricken Dandelion car and that he was subsequently airlifted to a hospital via helicopter for further checks.
The 26-year-old is understood to have reported back and chest pain after the incident and is expected to miss next weekend’s SUPER GT race at Suzuka, where he was due to drive a Team Kunimitsu Honda NSX-GT alongside Naoki Yamamoto.
It is believed that Makino avoided any major injuries and will be discharged from the hospital on Monday.
Apart from Lawson and Makino, B-Max driver Nobuharu Matsushita and Impul’s Yuhi Sekiguchi were also involved in the melee, which caused the race to be red-flagged
Matsushita, Sekiguchi and Lawson all escaped the incident without any injuries, with Lawson even able to take the restart after getting his car repaired under the red flag.
The race was won by Nojiri, with the result helping him return to title contention ahead of the title-deciding races at Suzuka in October.
Lawson finished over a minute down in 13th place after serving a drive-through penalty for getting his car repaired under the red flag.
