The British and Italian defence giant, Selex ES, is one of the "major funding partners" of the festival, which opens in two weeks' time.
The firm helps fund festival visits to one quarter of Scotland's primary schools each year and sponsors a "rampaging chariots race" for robots, expected to attract 6000 children at this year's festival.
The £3 billion company sells weapons and missile electronics to the United Arab Emirates, weapons management systems to Malaysia and Thailand, unmanned surveillance drones to Saudi Arabia, Jordan and Pakistan, and radar for use in Israeli drones.
Selex ES, which has a base in Edinburgh, specialises in high technology electronics and is owned by the major Italian firm, Finmeccanica, the world's eighth-largest arms company.
Scientists, politicians and campaigners against the arms trade say it is wrong for a festival aimed at children to be backed by a firm whose products "cause death and destruction around the world." A petition has been launched and "Disarm the Science Festival" protests planned.
The Sunday Herald understands that Selex ES's sponsorship is also causing dissension within the festival hierarchy. One of its board of directors, Rev Ewan Aitken, a long-time peace campaigner and former Labour leader of Edinburgh Council, is planning to make his concerns known at a debate on April 18 during the festival.
Dr Stuart Parkinson, the executive director of Scientists for Global Responsibility, which brings together 1000 professionals, accused Selex ES of selling weapons to governments with poor human rights records.
Dr Parkinson said: "This is not a good example for our children," adding: "The public endorsement that implicitly comes with the sponsorship of the Edinburgh International Science Festival helps them to paint a positive image - and it is something they do not deserve."
The Campaign Against the Arms Trade was "extremely disappointed" the festival was retaining its relationship with Selex ES. "The company has been involved in arms sales to repressive Middle Eastern regimes," said the campaign's Miriam Dobson.
"While we believe science should be about making the world a better place, the festival's support for Selex ES - including allowing the company to run workshops for children - suggests that it does not share our view. This is deeply concerning."
Green MSP Alison Johnstone warned that the science festival was putting its excellent reputation at risk. "The projection of military aggression in our society must be tackled in every possible way, and I would strongly urge the festival to play its part and rule out accepting such donations in future," she said.
The Science Festival confirmed that it received £18,000 a year from Selex ES, and that the company staffed robotics workshops. "In an unstable world, defence companies are regrettably a necessary and legitimate part of life," said the festival's director, Dr Simon Gage.
"We are prepared, guided by our ethical policy, to have relationships with this industry, which is why we have a partner in Selex ES - a major employer of scientists and engineers in Scotland. Their support of us is thematically neutral and provides a great educational experience."
Gage pointed out that objections to the company's role had prompted the festival to stage a debate this year on the role of scientists in the defence industry. "This will bring representatives from both sides together to discuss this unquestionably emotive issue," he said.
Selex ES insisted that it would not sell its products to countries that failed to comply with UK Government export rules. "An export licence will not be issued where it is judged that there is a clear risk that the proposed export might be used for internal repression," said a company spokesman.
"Selex ES strongly supports the UK Government's approach to export sales and will not sell its systems and technology to customers that do not meet these right and proper criteria," he added.