Of the GPs who used the system, 34 per cent said they experienced problems once a week, 9 per cent once a fortnight and 6 per cent once a month.
Only 6 per cent of the GPs said they had not experienced any problems, although these GPs had each only used the system once.
Over 70 per cent of the GPs with Choose and Book software had used it to book appointments. Of these, 42 per cent said it took them at least 10 minutes, 36 per cent five to 10 minutes and 22 per cent less than five minutes.
Professor Mike Pringle, joint GP clinical lead for Connecting for Health, which is in charge of Choose and Book, said: 'This is a transitional phase and it is more difficult for some practices to integrate than visualised.'
He added that those GPs who used the software frequently reported that it was 'easy to use'.
Wessex LMCs chief executive and GPC member Dr Nigel Watson, who has been using the Choose and Book software since October, agreed. 'The more you use it, the slicker you get,' he said.
Following problems with the system over Christmas, he stopped using it for three weeks and then found himself pressing the wrong buttons.
He added that not all the problems were related to GPs' lack of familiarity with the system.
'Sometimes it is frustrating because it does not work,' he said.
Last Saturday, Dr Watson went to his surgery to use the system to make some bookings and could not connect.
He said he knew that improvements were being made to the software, but said the bandwidth also needed to be increased.
'It needs to be instantaneous,' he said.
GPC negotiator Dr Richard Vautrey said the results showed that Choose and Book was 'not yet good enough', but he hoped there would be increased imperative to resolve glitches as more people used it.
'It is unacceptable for practices to be using something that is not as good as it should be,' he said.
Dr Vautrey expected that in some cases the problems were due to inadequate hardware that needed upgrading.