Stoner's announcement at Le Mans that he will retire at the end of the year has left Honda with the massive quandary of finding a suitable replacement.
Yamaha's Jorge Lorenzo, Ducati's Rossi, last year's Moto2 runner-up Marc Marquez and a multitude of other riders have been connected with the factory ride.
Nakamoto says HRC will not rule out any options, and that the first step will be to speak to current works rider Dani Pedrosa, who is in his seventh straight year with the squad.
"I need to gather my ideas and discuss with my bosses in Japan," Nakamoto told Motosprint. "Nothing is impossible now.
"First of all I want to talk properly to Dani because he's very strong and he's been with us for many years. We can talk to Lorenzo, obviously. With Casey leaving we need to rebuild."
Asked whether Rossi could rejoin HRC, with whom he split acrimoniously at the end of 2003, Nakamoto refused to rule out the possibility, saying: "After all, Valentino started his career in the top class with Honda."
He also admitted there was pressure from sponsors Repsol to give Marquez the ride, but insisted that it would be dependent on Dorna's Carmelo Ezpeleta reversing the rookie rule and that HRC did not want to pair two Spaniards together.
"[Marquez] is the rider Repsol wants to invest on, but to find out how we'll place him you need to wait for Carmelo Ezpeleta's decision regarding the rookie rule. But HRC will not have two Spanish riders together."
Nakamoto said he did not think Stoner would change his mind, but said HRC would take its time about choosing a replacement for the reigning world champion.
"Maybe after spending one year in Australia he [Stoner] may feel nostalgic. Few things in this world give you the adrenaline you get from racing. After all, he'll turn 27 in October: even if he stayed out for one or two years he could come back before he turns 30 and he'd still be strong.
"My mission in 2009 was to make HRC strong again in every aspect, and my job hasn't ended. When I decided to hire Stoner, no one had anything against it: let's see what their thoughts are now.
"It's really early to make plans, because there are many things to evaluate. It's easy to talk and make predictions, but then to put it all into practice is a lot more complex because everyone's needs must be considered: companies, sponsors, riders.
"And besides, Honda is not in such a hurry to decide: we can take our time to think calmly."