The Connect programme, which went through design and build phases and into testing in 2014, has been created to improve customer service and efficiency.
The FSCS said in its annual budget report this week it would spend £3.6m in 2015/16 on the next phase.
The programme is due to go live in April 2015.
The report showed the rising costs of the project, stating: "The Connect programme had lifetime external cost as approved by the Board subcommittee in August 2013 of £12.2m. This increased to £15.7m during 2014 due to additional design requirements and the current predicted spend on the programme is £20.4m.
"This incorporates document scanning and transmission, increased testing and streamlining the data exchange with the outsourcers.

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"This is being funded by savings and contingencies in other projects and the reprioritisation of work combined with lower spend on Keydata and other recovery expenditure which has not materialised throughout the year.
"The first phase is now planned to go live in the Spring of 2015."
The organisation said that the scheme would ultimately benefit both consumers and levy payers.
Connect will allow people to complete applications online and give them more choices when interacting with FSCS, officials said.
The FSCS said in its report: "In preparation for going live, FSCS has started to reorganise its structure. Recruiting the people we need to complete the new organisation is already more than ninety per cent complete. A number of people have also left the organisation and we thank them for their service and wish them well for the future.
"Going live will not only mean the ability internally to operate on the new platform with new processes, but also provide the same capability for our business process outsourcers (to be rolled out after go live).
"Most importantly, going live will also mean the launch of our online claims system. This will allow claimants to interact with FSCS electronically and to submit claims online for the first time."   

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