Spain's Jorge Martin (left) leads the back on his way to winning the MotoGP race in Motegi, Tokyo, on Sunday. AP

Jorge Martin narrowed the gap on championship leader Francesco Bagnaia to just three points after winning the rain-affected Japan MotoGP on Sunday.

Bagnaia came second and Marc Marquez took third, leaving the leading duo to battle for this year's crown with six races to go.

The 24-lap race began under overcast skies, and when the rain intensified organisers suspended it with 12 laps to go.

They attempted a restart, but the race was quickly called off and the riders were awarded full points according to their positions at the stoppage.

Martin said he felt in strong command of his bike even in the rain, but was happy to collect the points and ready to move on to the next race.

"I am so happy," Martin said. "Luckily everyone was OK."

Spain's Jorge Martin celebrates after he won the MotoGP race in Motegi, Tokyo, on Sunday. AP

Bagnaia said he thought he could have overtaken Martin, but also voiced his relative satisfaction.

"Jorge gained some more points. But I am very happy," he said.

"Unlucky, we had (the) possibility to win. But in any case, I'm happy with the position."

Agence Frane-Presse