These areas are Liverpool, Hastings, Bristol, Staffordshire and South Worcestershire.
However, despite this, Hancock said he believed the NHS infrastructure was moving in the right direction - and that the NHS has learnt about delivering cutting edge technology in very complicated settings with big legacy systems.
The code clarifies expectations from suppliers of the technology, and how the government will support innovators in health and care, including development of trusted approval systems and a coherent pathway for suppliers to enter the market.
"Yet our hospitals operate dozens of systems each, that don't talk to each other".
"The net result is not just scarce resources wasted but countless hours of clinical staff spent trying to work broken systems, patients being given suboptimal care because systems didn't communicate and ultimately lives lost".
Meanwhile, NHS England plans for all patients in England to be able to download the app from the end of December, with access to limited features.
Ian McGregor, vice-president of the software company UiPath, said: "The pledge of a £200 million fund for NHS trusts to assist technological transformation in the health sector is welcome news".
The Secretary of State also announced the creation of the HealthTech Advisory Board, chaired by Dr Ben Goldacre, which will report directly back to him.
Hancock explained that the current IT systems are not fit for the future, and that both major investment and an overhaul of services is required in order to enable the NHS to cope with increasing demand.
"Now is the moment to draw a line and put the failures of the past behind us and set our sights on the NHS being the most cutting-edge system in the world for the use of technology, to improve our health, to make our lives easier, and to make the money go further".
Shadow health secretary Johnathan Ashworth said it was "astonishing" that rather than prioritising dealing with staff shortages or ever-growing waiting lists in the NHS, "the health secretary is insisting new IT systems must be paid for by already over-stretched budgets".
"I want the best for the NHS, and will do all I can to make that happen. We need to make the most of that money", he said.