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."
Nintendo is facing more complaints about its new console, Switch, this time about the controllers failing to connect.