The company said it was looking into the matter, which could be caused by wireless interference, and suggested gamers sat closer to the console.
It comes after some players complained about their screens containing dead pixels that created black squares.
The console has received largely positive reviews and is selling well.
Reports about problems with the controllers, known as Joy-Con, have been around since before the launch of the console, among those who had pre-release review units.
It seems to affect play when the console is connected to the TV and the controllers are being used wirelessly.
On its support page, Nintendo advised users to make sure that the Switch console was placed "out in the open" and not behind a TV, in or under a metal object or near an aquarium.
It also advised users to make sure the console had the latest software update and to "try to decrease the distance" between the Joy-Con and the console.
The problem seems to be worse in the left-hand controller and some, including games writer Jeff Gerstmann, report it is affected by how close users sit to the TV.
A video posted on YouTube suggested that while the right-hand Joy-Con had a dedicated antenna, the left-hand one was harder to find.
"The antenna is printed directly on the controller's circuit board; it's not a separate unit inside the device. Second, the antenna is located beneath the controller's shoulder button and next to the housing for the controller's joystick," said gaming website Polygon.
"All of that could block or weaken the Bluetooth signal," it added.
A straw poll on the social media platform Reddit suggested that 20% of respondents (out of a total of 6,300) had experienced some kind of issue with their Switch console.
Piers Harding-Rolls, an analyst at research firm IHS Markit said: "Obviously, if this does occur when gaming it can be frustrating, but generally I don't think this is impacting people's enjoyment of the platform too heavily."
"What is perhaps making it worse is that the right Joy-Con has better connectivity which is highlighting the left's relative weakness.
"If this is a design issue, I expect Nintendo to look closely at adjusting the lay-out of the antenna in the left Joy-Con to help solve the issue, as the fix would appear relatively straightforward."

The three-year-old, ridden by Adam Kirby and trained by Clive Cox, is part of Sheikh Mohammed's Godolphin team.
Last year's winner Limato was second, a length and a quarter behind, with Brando in third.
Aiden O'Brien's Caravaggio, a heavy favourite who beat Harry Angel in June's Commonwealth Cup at Royal Ascot, finished fourth.
Harry Angel made a solid start and tracked Caravaggio's pacemaker Intelligence Cross in the early parts of the race before taking the lead in the final furlongs.
Caravaggio, ridden by Ryan Moore, went into the race unbeaten with six wins out six but never looked like bridging the gap, as Harry Angel won by an impressive length and a quarter from Limato.
"He's always been special. We always hoped he'd be Group One material and he is," said trainer Cox.
"It's great to get a winner for Sheikh Mohammed on his birthday. Today I was very confident about his whole demeanour, it's just a joy to be involved with top-flight horses."
Jockey Kirby added: "He's the best. He's gone from a boy to a man with every race he's had."
Cornelius Lysaght, BBC horse racing correspondent
The first major contest between the three-year-olds and the older horses - in the Eclipse Stakes a week ago - went narrowly to the seniors. This result boosted the younger lot emphatically. In this division, they're pretty good.
Clive Cox was convinced Harry Angel had not just come out well following his defeat by Caravaggio at Royal Ascot in June, but that he had flourished since, and that's what was demonstrated.
Continuing a fine year for the Godolphin string, Harry Angel, bought by Sheikh Mohammed before Ascot, swept aside his rivals, with Caravaggio - part of the operation of Coolmore, Godolphin's arch rival - only fourth here.
Nintendo is facing more complaints about its new console, Switch, this time about the controllers failing to connect.
[NEXT_CONCEPT]
Harry Angel won the prestigious July Cup in brilliant style over six furlongs at Newmarket.