In a letter read out in parliament on Friday, Thein Sein said the $3.6bn (£2.3bn) Myitsone dam was contrary to the will of the people and lawmakers.
Pro-democracy leader Aung San Suu Kyi recently joined the anti-dam campaign.
The suspension is being seen as a rare victory for social and political campaigners, says the BBC's Rachel Harvey in Bangkok.
It also marks a further indication by Burma's new government that it wants to take account of public opinion and seek greater legitimacy, correspondents say.
The Myitsone dam project was being developed jointly by Burma and China at the head of the Irrawaddy river, in an area currently the scene of conflict between government forces and ethnic minority insurgents.
A broad spectrum of political activists, conservationists, academics and international bodies had opposed the project.
Their objections ranged from the lack of public consultation to the potential environmental impact of a project that would have created a reservoir about the size of Singapore and forcibly displaced thousands of ethnic Kachin villagers, our correspondent says.
"The president sent a message comprising 10 points to the parliament this morning. One of them said that the construction of the dam on the Irrawaddy will be shelved during the term of his government," one official at parliament was quoted by Reuters news agency as saying.
"He said that his government, being born out of people's desire, has to act according to the desire of the people," said the official, who declined to be named because he was not authorised to speak to the media.
The U-turn will be seen as a victory for Aung San Suu Kyi, commentators say - and a blow for conservative elites with links to Chinese investors who had backed the project.
The vast majority of the electricity produced on the dam would benefit China, and the dam had served to inflame growing anti-Chinese sentiment in Burma, our correspondent says.
Beijing is investing vast sums in a series of big infrastructure projects aimed at exploiting Burma's rich natural resources and geographic position in the region, she says.
There has as yet been no official reaction from China to the unusual step taken against it by its isolated ally.