Out of 327 GPs and practice managers who responded, 76% said that when payments arrive, they struggle to identify what they relate to.
GPs across England experienced problems with payments following the overhaul of NHS organisations from April 2013.
Plans from NHS England to cut by £40m the cost of back office services that administer payments to practices have also left GPs concerned that support over payment queries would suffer.
NHS England said earlier this year that improvements to its National Health Application and Infrastructure Services (NHAIS) tools had made it easier for practices to match payments with services delivered.
Problems with payments
But the findings suggest practices are continuing to experience problems identifying payments.
Many practices looking to query payments say they do not have a named individual to contact within their NHS England area team.
Under PCTs, 55% of GPs and practice managers say they had a named contact to approach for help with payments. But only 17% say they can contact a named individual within an NHS England area team now.
GPC deputy chairman Dr Richard Vautrey: 'These are basic things practices depend on, particularly practice managers. They really should be getting it right by now.'
He warned that as NHS England puts the payments administration service out to tender as part of the drive to deliver savings, it would need to ensure a 'quality service for practices'.
He added: 'It can be quite complex for practices to identify payments - they can come from the local authority, NHS England, CCGs. Sometimes it is not clear why a payment has arrived, and practice managers have to try to track what relates to a particular activity. This is taking a substantial amount of time for practice managers.'
NHS England has yet to respond.