Lewis Ludlam, Courtney Lawes, Freddie Steward and Joe Marchant touched down and it was only when their fullback had collected a George Ford chip and stormed over in the 67th minute that they looked comfortable.
Lawes' try came after the ball had taken a comical bounce off Joe Marler's head and while England celebrated their first World Cup tries since their 2019 semi-final victory over New Zealand, a madcap Sunday evening in Nice posed fresh questions.
Early in the second half they were booed by their own fans as they continued to kick the ball away at every opportunity, only to then throw the kitchen sink at enterprising opponents ranked 14th in the world.
The ambition paid off and with Ben Earl and Steward propelling them forward as well as impetus coming from Marcus Smith's arrival off the bench, they stormed out of sight.
After routing Argentina 27-14 with 14 men in their Pool D opener, they at least avoided a potential banana skin and with fixtures against Chile and Samoa to come, they are destined to reach the last eight.
It took England half an hour to fire their first shots, launching Manu Tuilagi in midfield and Earl into the wall of red and white shirts, but until then they had displayed little endeavour.
Half-backs Ford, who booted 14 points, and Alex Mitchell seemed content to continuously kick the ball away, perhaps convinced that the humid conditions meant it was wiser to wait for Japan to make a mistake.
That is exactly what happened in the 25th minute when Ford steered a clever chip into the left corner and the underdogs botched the line-out, enabling Ludlam to pounce from short range.
Japan fullback Semisi Masirewa had been lost to an innocuous injury in the eighth minute but with Rikiya Matsuda kicking three penalties, they trailed just 13-9 at the interval.
The second half started at a ferocious pace, but the ball continued to slip out of the hands of players from both sides.
England's first instinct remained to kick, with Mitchell drawing boos when he booted the ball dead, but they were at least pinning Japan back in their own half and showing signs of building momentum.
Tension mounted as the Brave Blossoms escaped their own territory and claimed three more points from Matsuda, but when Earl went tearing down the right wing and the ball was recycled for Lawes to collect and score, their chances seemed to be fading.
Play swung from end to end and suddenly England were scrambling furiously, but Japan missed their chance and were made to pay when Steward caught Ford's kick and strolled over. Marchant delivered the final blow in the closing moments.
