Bloggers first spotted that smoke on Adnan Hajj's image of the aftermath of an Israeli air strike in Beirut appeared to have been made darker.
A Reuters investigation confirmed this and also found two flares had been added to an image of an Israeli jet.
Mr Hajj told the BBC he denied doctoring the content of the images.
He said had tried to clean dust off the first image, a shot of buildings in a suburb of Beirut, on which Reuters found smoke plumes had been darkened and expanded using computer software.
"It was so badly done - an amateur could have done better," Bob Bodman, picture editor at the Daily Telegraph newspaper, told the BBC.
Mr Hajj, a freelance photographer working for Reuters, denied altering the second photograph, an image of an Israeli F-16 fighter over Nabatiyeh in southern Lebanon.
"There's no problem with it, not at all," he said in a BBC interview.
'Lapse'
Paul Holmes, editor of political and general news at Reuters, told the BBC that senior photographers at the agency "weren't convinced" that cleaning dust off the first image would result in the manipulation the image showed.
He said there had been a "lapse in our editing process", but stressed that Reuters had moved swiftly to address the issue and tighten editing procedures.
THE EDITORS' BLOG
Global picture editor Tom Szlukovenyi said all of Adnan Hajj's images had been removed from the company's database.
He described it as a precautionary measure, but said the manipulation undermined trust in Mr Hajj's entire body of work.
"There is no graver breach of Reuters standards for our photographers than the deliberate manipulation of an image," Mr Szlukovenyi said in a statement.
Questions were raised about the accuracy of the image on Sunday in several weblogs - personal online diaries by writers known as "bloggers" - including ones which scrutinise media coverage of the Middle East for bias.
Mr Holmes said Reuters welcomed the growth of weblogs, which had made the media "much more accountable and more transparent".
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