Nearly 200 GP partners took part in the poll, 46% of whom said they were currently having problems with Capita.
A total of 56% of respondents said they had experienced issues with pension payments over the past year, while just over half (52%) had trouble with patient record transfers.
Other common sticking points for partners over the past year included problems with rents and reimbursements (32%), the performers list (24%) and enhanced service payments (23%).
The findings come just months after NHS England announced plans to review all GP pension data after 'discrepancies' were found between contributions and pensionable earnings.
Since taking responsibility for Primary Care Support England (PCSE) in 2015, Capita has faced criticism over administrative errors that have affected GP workload and raised questions about patient safety.
Last year the BMA hit out at an 'appalling' failure by Capita to deliver cervical screening letters to 48,000 women in England.
A report by MPs said the decision to outsource PCSE services to Capita was a 'shambles' and asked NHS England to write to the House of Commons public accounts committee to explain what steps have been taken to compensate primary care practitioners for the disruption caused.
GP leaders have repeatedly called for the government to end the contract with Capita and take primary care support services back in-house.
The GPonline poll found that the proportion of all GPs reporting ongoing problems with Capita - around a third - was almost unchanged compared with a similar poll last year.
A Capita spokesperson said the company had initially underestimated the challenge that delivering primary care support services would pose, but that it was determined to get the service right.
GP partners responding to the survey branded Capita’s PCSE service ‘inadequate’ and ‘a complete mess’, with many voicing frustration over delays and communication problems.
One GP partner said it had taken them ‘six months or longer to get patient records’ under Capita, while another said that out-of-date or incorrect pension payments were ‘preventing me from taking the decisions I need to take about retirement’.
A third GP asked when Capita would face consequences for problems with primary care support. 'If GPs make even the tiniest error or introduce any delay in delivering our services we are put through the mill with our livelihoods on the line,’ the GP said.
GPC chair Dr Richard Vautrey said: ‘It's a real concern that so many GPs and practices continue to be so badly let down by Capita's PCSE service. These problems cause day to day difficulties and lead to practice managers and others spending significant amounts of time trying to sort them out when they should be focusing on other important practice matters.
‘It's why GPC have called on NHS England to end the contract for this service as there appears no end to the problems practices have had to cope with since Capita took over.’
A Capita spokesperson said: 'We have acknowledged we initially underestimated the complexity of this contract. Improvements have been made, and we continue to work with stakeholders and customers to ensure awareness of correct processes to follow to access services.
'Capita is committed to getting this contract right so we can carry on saving the health service money and help NHS England deliver their objective of transforming locally managed, manual paper-based operations into a modern and efficient national customer-focused service.'
NHS England did not wish to comment.