Honda rider and current championship leader Marquez will start Sunday’s race in pole position with Ducati’s Jack Miller in second and KTM’s Johann Zarco in third.
But Suzuki rider and fellow Spaniard Rins, who will begin in fifth spot 2.617sec behind Marquez, was angered by what he saw as Marquez altering his line and making contact with him during the second session of the day.
“I think he has no respect for the other riders. He is riding on his way,” Rins said.
“On Turn five, he went a bit wide, and behind him was Miller and me. When we went wide, he looked behind and he saw Jack and me.
“Jack passed him, but he went (back) into the (racing) line. And sincerely, he disturbed me.”
Marquez, 26, defended his manoeuvre at a circuit where has chalked up two wins in 2013 and 2017.
“If he (Rins) thinks this, well, I do not agree with this but this is his opinion,” he said.
“I tried to follow Jack because he had a good pace and then I went a little bit too wide and there was little space and we made small contact (with Rins) but to me it is racing.”
Suzuki have also filed a complaint against Marquez to the race organisers echoing their rider’s comments.
“He is a very talented rider but he should have more respect for his rivals,” Suzuki said.
“He has done it more times in his career and he has been sanctioned.”
It was a sixth pole of the season for Marquez, who finished 2.524sec ahead of Australian Miller.
‘I took all the risks’
In difficult weather conditions at the end of the second session Marquez was the first to dare to change tyres to deal with the rain.
“I took all the risks, even if my team wasn’t happy about it,” he told French broadcaster Canal+.
Miller, 24, said a slow change to slicks was to blame for missing out on a second pole position for the season.
“All in all a reasonable day even if I ended in the gravel trap. It took me 20 seconds more than Marc to switch to dry and that made the difference,” he said.
Marquez has notched up five victories from the nine races of this 19-race season and sits 58 points clear of Italian Andrea Dovizioso, who won in Brno last season.
Seven-time championship winner Valentino Rossi is one behind Dovizioso in fifth place at a circuit he last tasted victory a decade ago.
“These conditions are always difficult for us, we struggle very much, so starting from the third row is not so bad,” Rossi said.
“I hope for a dry race tomorrow and also for a dry warm up, because we have a lot of things to try, especially to make the right tyre choice,” he added.
Marquez last year finished third behind Ducati’s Dovizioso and Jorge Lorenzo, who has since become his teammate at Honda.
The weather forecasts further rain and storms during the race.