Rins and Nakagami were battling for 12th spot in the early stages of Sunday's race at Mugello after a poor qualifying left the Suzuki rider down in 21st on the grid.
Attempting to pass the LCR rider on the inside of the Turn 11 left-hander on lap seven of 23, the pair came together and Rins crashed out, marking his second-successive DNF.
Rins fumed after the race about the collision and took aim at the Stewards' decision not penalise Nakagami.
"How I feel about Taka? Sincerely I don't understand what he did," Rins said after the race. "I saw a video and sincerely he was out of the line. The lap before I tried to overtake him in the same corner, between 10 and 11 and he held the position.
"So, the next lap I tried to push a little bit more with the throttle to be more in front of him and he was outside, and when we did the corner he was there and we impacted.
"It's a clear example of what [Johann] Zarco did with [Marco] Bezzecchi. Zarco put the bike [up the inside] and Bezzecchi lost the position, so he rolled out of the throttle a little bit.
"I don't understand the decision of the stewards. They say that I was not in front of him and they will not penalise him.
"If you ask the riders, he is one of the most dangerous guys on track in terms of overtakes.
"But it is what it is. Luckily nobody was behind us. But I don't understand the way he goes."
Rins added that the incident will be talked about in this week's safety commission at the Catalan Grand Prix.
"I didn't speak to Taka yet," he said. "For sure it's a thing to comment on in the safety commission because clearly the stewards don't do the right work.
"I go there to speak with [FIM Steward] Freddie Spencer and I say to him 'mate, you are an ex-rider, you did a lot of overtakes and there is no regulation in the books that says when someone overtakes you, you need to close the throttle'. It's just a thing with the riders.
"So, I don't understand why Taka did this and that's all. Was super, super dangerous. We are in MotoGP, we don't race like this."
