Morrisons' £310m upgrade of its IT systems has hit problems, which industry sources have warned could have a knock-on effect on availability in-store.

The supermarket has been carrying out a comprehensive upgrade of its systems since 2007, shortly after former CEO Marc Bolland joined the business. The upgrade has recently been rolled out to its manufacturing side and is understood to have been dogged by corrupt data.

The Grocer has learnt the data is being processed in the wrong order and both Morrisons and Oracle, which is carrying out the IT overhaul, are trying to work out why. Other issues include staff struggling to get to grips with the new system and software quality.

"It is a very big problem," said one senior industry IT expert. "They are struggling to understand why it is not processing in the order it should. It could affect orders and have a knock-on effect on supply."

Another senior industry source added: "Morrisons appears to have major data and process issues in its manufacturing process. The key issues seem to be process compliance, software quality issues and data integrity issues. This could be impacting production into stores."

Morrisons revealed in 2007 that it planned to overhaul its IT systems, at a cost of £110m, because they were "approaching the point of requiring to be changed" with some up to 30 years old. In March this year it said the next stage of the project, focusing on manufacturing and warehouse systems and due to run until 2013, would cost an extra £200m.

However, Morrisons' IT director Gary Barr played down the problems. "At this stage, we are testing new systems for our manufacturing in one pilot site," he said. "We are delighted with the progress made and the robustness of the system implemented.

"Clearly, we will make tweaks to our approach coming out of any learning from our pilot but these will be only minor as the system installed is performing as intended and continuity of supply has been maintained throughout we are now beginning to see the benefits we expect."