Last week, North Central London PCT cluster admitted having problems with payments to practices across all of the five boroughs it covers.
GPC deputy chairman Dr Richard Vautrey has urged practices to contact their PCT clusters if they notice problems with payments arising from the 'chaos' of PCT reorganisation.
'This just shows some of the chaos going on at the moment with tasks not being done properly,' he said.
'Practices need to get on to their PCT clusters and ask them to pull their finger out.
'It is the PCT cluster's responsibility to deliver its basic function of making payments to its providers,' he added.
Londonwide LMCs medical director Dr Paddy Glackin said practices had found out about the problems by checking their bank accounts.
'Things are falling through the net,' he said. 'People are hugely overstretched and mistakes are being made. The question keeps arising because we have fewer people carrying out five boroughs' work than used to do one.
'I am sure it is happening all over the country. It means practices are not 100% certain what they are getting or that they are being paid in a predictable manner.
'Practices should be careful. They need to know what they should be getting paid and check it is going in.'
North Central London cluster said most payments had been timely and accurate, and that practices had been given contact details for PCT staff who were dealing with practice payments.
'We are rolling out an electronic system that enables the practice to have real time data on what payments we have made, and for what service,' a spokesman said.