Variations in commissioning budgets could prevent CCGs from working together to mediate risk.
Bury CCG Chair Dr Kiran Patel told MiP his plans to develop a federated commissioning model with a number of CCGs in the Greater Manchester area could be placed in jeopardy as he fears funding variations could create tensions between commissioners.
"Board members could be put off from wanting to pool resources with other CCGs if they had more money to play with," he said.
"It is crucial for CCGs to work together to harness their spending power and mediate risk.
"This unfair formula used to decide funding allowances needs to change if CCGs are to be free to work together."
The CCG indicative funding allocations document is expected to be released in February following a number of delays.
Dr Hugh Reeve, Chair of the Cumbria CCG covering over 500,000 patients, told MiP any CCG Chair hoping for "significant" movement in commissioning funding allocation "is living in cloud cuckoo land".
"I would be very surprised if CCG funding is moved to where is should be considering PCTs have been having to cope with being overfunded or underfunded for a decade," he said.
"Any big movement in funding is also likely to be very destabilising for general practice."
Dr Reeve did, however, acknowledge that variations in funding may lead to CCGs "going it alone", but said "there are plenty more reasons for commissioners to work together apart from money".