The e-booking system developed for the NHS national programme for IT (NPfIT) is running behind schedule as a result of "early stability problems with the central system".
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Choose and Book, the e-booking system for booking hospital out-patient appointments, is being tested at four early-adopter sites in a pilot programme that began in August.
But "fewer than 100" live bookings had been made on the system, a spokesman for the NPfIT said on Monday.
The spokesman added that, "Although there have been fewer bookings than we had aimed for, we are not widely off our mark and are not behind for achieving the roll-out."
The NPfIT said the core technology for the system is in place and has been tested to manage 500 million appointments a year. "Bookings are being made by all the early adopters," the NPfIT spokesman said.
Plans for a second set of early adopters to participate in the program in the fourth quarter will probably be postponed until January at the earliest, the spokesman admitted.
NPfIT will not name the four current participants, although Barnsley Primary Care Trust is known to be a participant.
Atos Origin won the primary contract for the system last year, and US firm Cerner provided the software.
The system is designed to handle 13 million outpatient consultations, four million emergency admissions and 617 million prescriptions, according to Cerner.
Meanwhile the British Medical Association (BMA) expressed its concerns about the privacy of the e-booking system. It has warned that GPs may boycott the system if they are not convinced that the confidentiality and security of patient records are beyond reproach.
"A Choose and Book appointment cannot be concluded until an electronic referral has been made by the GP. At the moment it would be impossible to do so confidentially as electronic referrals are not yet coded in a way that keeps them secure," said Dr Laurence Buckman, deputy chairman of the BMA's General Practitioners Committee.
The NPfIT claims the system is secure but conceded that more needs to be done to engage the doctors and other staff who will use the technology.
The chairman of the BMA's IT committee said earlier this month at the eHealth Conference in London that the NPfIT's engagement and consultation with the medical profession has been inadequate.
One hospital administrator who asked not to be named said that she and her group were having difficulty working out kinks in the system - due in large part to a lack of communication between all of the parties involved.
She said that since her department started using the e-booking system in May there had been a lack of consultation between the NPfIT and those using the system on a grass roots level.
Laura Rohde writes for IDG News Service