Fujitsu was contracted to roll out the electronic patient records system to the south and south west of England, under a 10-year contract worth £895 million.
But CfH is to terminate the contract, after failing to agree a price for changes.
BT is favourite to replace the Japanese group, because it uses the same software.
But the changeover is likely to further delay the summary care record programme, which is already running four years behind schedule.
Fujitsu is the second supplier to leave the programme, after Accenture withdrew in 2006. It says it will continue to work to the original contract terms while a replacement supplier is found.
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