Fifth place in qualifying for the Spanish Grand Prix is Rossi's best grid position since returning to Yamaha. He was 0.822 seconds off pole in France.
"Like the other races, in the qualifying I am unable to do what I want," said Rossi.
"When I try to push more I create some problems with the bike.
"The other riders are better than me at using the extra grip from the new tyre, so I have to start from the third row.
"My rhythm is not so bad so we have to try to fix something."
Rossi said a tyre issue in Saturday morning practice had put him off his stride for qualifying.
"Unfortunately today was a worse day compared to yesterday," said the Italian, who had been optimistic on Friday after outpacing team-mate Jorge Lorenzo.
"We started quite badly this morning because we had some problems with the rear tyre so we struggled very much in the practice.
"We had a lot of question marks so we wanted to try the same setting this afternoon. In fact the tyre had a problem because this afternoon it was not so bad."
He fears the usual top three riders will be out of reach again in the race.
"My rhythm and pace for the race is quite good, unfortunately especially Lorenzo, [Marc] Marquez and [Dani] Pedrosa are a bit faster," said Rossi.
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