The allegations against the news agency have been made by a number of blogs including Little Green Footballs, one of the many sites that in 2006 helped expose image doctoring by a freelance photojournalist working for Reuters.
The blog shows two photos as published on other websites and compares them with how they appeared when published by Reuters, claiming a knife in the hand of an activist has been cropped out of each picture. Questions have been raised over whether protestors on the ship were armed and what impact this could have had on the actions of the Israeli troops on board.
The agency has said the absence of the activists holding knives in the pictures it originally published to its wire was an editing error.
"Reuters is committed to accurate and impartial reporting. All images that pass over our wire follow a strict editorial evaluation and selection process. The images in question were made available in Istanbul, and following normal editorial practice were prepared for dissemination which included cropping at the edges," the agency says in statement given to Journalism.co.uk.
The uncropped images have now been reinstated as part of the agency's package of images from the aid ship attack.