The BMA reported this month that around 2,000 GP practices 'did not have pension deductions taken for one or more GPs from June to August' this year.
PCSE has told the BMA that most of the delayed deductions would be collected from September's payment runs - meaning practices face paying pension contributions for several months in one go.
Accountants have warned that the surge in pension charges this month could trigger cashflow problems for some practices, particularly if they were unaware of the shortfall in deductions - and could force partners to reduce their take-home pay temporarily.
Deborah Wood, a partner with MHA Moore and Smalley and chair of the Association of Independent Specialist Medical Accountants (Aisma), told GPonline: 'This is largely a timing issue but could have a short-term impact on practice cashflow, particularly if practices think they are earning more than they actually are, due to higher payments without pension deductions hitting practice bank accounts.
'Some practices still pay drawings to their GP partners based on actual practice cashflow for the month, so that could lead to some GPs having to go with lower than expected monthly payments in the months that PCSE actually take the pension contributions due.'
The delayed collection of pension payments by PCSE - a service outsourced to private provider Capita - is the latest in a long line of problems.
In June the BMA warned that as many as 1,000 GP practices were still waiting for the previous year's QOF acheivement payments, in some cases worth six-figure sums.
GPs have previously called for Capita to be stripped of its contract to run PCSE after problems with the service - and as far back as 2018 MPs said the decision to outsource the service had been a 'shambles'.
Ms Wood said collection of pension payments had been 'hit and miss' for some time, but that the transition to a new system earlier this year appeared to have exacerbated the problem.
She said problems had occurred when salaried GPs took on partnership roles, that pension deductions had continued after partners left practices, and that problems had occurred with basic data entry errors.
A Capita spokesperson said: 'During the migration from the NHAIS system to PCSE Online we identified that the NHS pensions scheme number for some GPs was missing, resulting in their pensions deductions not being properly linked to their practice.
'After engaging with NHS Pensions and NHS England to resolve this legacy data issue, pension deductions for these practices have resumed and any outstanding deductions processed. The transition to PCSE Online this summer means that all users can now manage their pensions and payments activities in a more connected and effective way.'