The decision follows reports in the US and South Korea of the phone "exploding" during or after charging.
The South Korean company said customers who had already bought the phone would be able to swap it for a new one.
Samsung said it had been difficult to work out which phones were affected among the 2.5 million Note 7s sold.
"There was a tiny problem in the manufacturing process, so it was very difficult to figure out,'' the president of Samsung's mobile business Koh Dong-jin told reporters.
"It will cost us so much it makes my heart ache. Nevertheless, the reason we made this decision is because what is most important is customer safety," he said.
The firm said it would take about two weeks to prepare replacement devices.
According to Samsung, the phone has been launched in 10 countries so far but with different companies supplying the batteries.
The recall comes just one week ahead of an expected presentation of a new iPhone model from its main rival Apple.
What makes lithium batteries catch fire?
This is an extraordinary decision for a tech giant to make based on so few reported incidents - Samsung says it is aware of only 35 cases worldwide.
It's bad timing so soon after a big product launch and especially given that Samsung's rival Apple is understood to be preparing to unveil a new iPhone.
However, the firm says it has discovered a problem with the battery cell and is halting sales while it inspects its suppliers.
People who have already bought the device - which is only available to pre-order in the UK - will be issued with a replacement.
Stories about exploding smartphone batteries do make the news from time to time - lithium ion batteries are flammable but very widely used.
Over the past few days, several users have reported their phones catching fire or exploding while charging, and Samsung said it had confirmed 35 such cases.
A YouTube user uploaded a video under the name Ariel Gonzalez on 29 August of a Galaxy Note 7 with burnt rubber casing and damaged screen.
He said the handset "caught fire" shortly after he unplugged the official Samsung charger, less than a fortnight after purchasing it.
Further images of a burnt Galaxy Note 7 were uploaded to Kakao Story, a popular social media site in Korea, on 30 August.
A user wrote: "There was another explosion of the Galaxy Note 7. It was my friend's phone. A Samsung employee checked the site and he is currently in talks over the compensation with Samsung. You should use its original charger just in case and leave the phone far away from where you are while charging."
The phone was only launched on 19 August and has since then been generally well-received by critics and consumers.
The Galaxy Note 7 model is the latest of Samsung's series of so called phablets - smartphones with very large screens.
Samsung also added an iris scanner to the Note 7, which lets users unlock the phone by detecting patterns in the eyes.
In July, Samsung beat expectations with record earnings in the latest quarter with strong smartphone sales helping the firm post its best quarterly results in more than two years.
Samsung had predicted continued increase in demand for its smartphones and tablets in the second half of the year.

This article was about:
Samsung Electronics is recalling its flagship Galaxy Note 7 smartphone and said that battery problems were behind phones catching fire.