The warning follows British Airway's decision earlier this month to split its IT department into separate operational and strategy arms.
The airline's former chief information officer, Brian Wilson, resigned following the restructuring. BA insists that the new divisions will raise the profile of IT within the business.
Andy Mulholland, chief technology officer at Cap Gemini Ernst & Young said a clear distinction between IT operations and strategy divisions could work well in industries going through relatively little change by allowing them to focus on driving down costs and overheads.
But he warned that creating the two divisions could delay IT projects at the eleventh hour due to operational and strategy staff working in isolation. "The biggest danger is that people who do the strategy and operations become two tribes and find it difficult to communicate," he said.
"Big IT projects could take longer to get right. You get to the launch quicker, but have a number of operational issues to sort out. Only programme managers, for example, understand the details of what is really needed."
Analysts said the operational and strategy split was logical and would highlight the importance of IT strategy across the business.
But they also stressed that having two divisions could damage staff morale, if the e-business-based strategy projects are seen as more glamorous than the back-office functions, run by the operations division.