Users began posting photos and videos on social media late last month showing the charred Galaxy Note 7 with part of its 5.7-inch touchscreen burnt and melted, saying it suddenly caught fire.
Samsung, the world's largest smartphone maker, said it would recall 2.5 million units shipped globally to countries including the US and South Korea, and offer new devices to existing users.
It is the first large-scale recall of one of Samsung's top of the range phones.
"We are deeply sorry for causing concern... And causing inconvenience among our users."
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He said the faulty rate amounted to 24 handsets per each million sold and that it would take about two weeks to prepare replacements.
The company has also been forced to delay the handset's planned release this month in several European countries including France.
The news comes as Samsung's archrival Apple is due to unveil its iPhone 7 on Wednesday.
The latest recall is expected to hurt its bid to outsell the iPhone 7, said Lee Jang-Gyoon, researcher at the economic think tank Hyundai Research Institute.
"Samsung released the Note 7 early to secure a leading position in the market in advance, but now the impact of the move will be blunted," he said.
Samsung currently uses batteries made by a number of different companies, including its sister firm Samsung SDI.
Samsung - South Korea's largest firm by value - posted a better-than-expected gain in net profit for the second quarter, boosted by solid sales of its high-end Galaxy S7 and S7 Edge phones and aggressive cost-cutting.
Today, shares were up 0.6 per cent after falling for two days in a row and after investors shaved USD 7 billion off the market value of the company on Thursday amid concerns about how the explosions would impact the firm's reputation.
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