After the failure of national negotiations, individual PCTs negotiated deals on payments for vaccinating healthy children aged under five years old.
None of the 116 who responded to a Freedom of Information request offered any payment above the £5.25 per jab agreed in the directed enhanced service deal for clinical at-risk groups.
However, some PCTs agreed to pay for vaccinating patients who were not in the clinical at-risk groups, but were deemed at risk by GPs.
Seven PCTs agreed to pay GPs for morbidly obese patients who did not fit into a clinical at-risk group.
NHS Blackpool agreed to pay GPs the normal £5.25 rate for vaccinating morbidly obese patients outside at-risk categories set out in the DES.
Dr Peter Higgins, chief executive of the Consortium of LMCs in Lancashire and Cumbria, helped negotiate the deal.
'We only got involved in local talks after the failure of national negotiations,' he said.
'We were able to get some more flexibility from the PCT. But we would much rather there were national agreements in these situations.'
PCTs' responses also revealed huge variations in how they set up antiviral collection points (ACPs).
A lack of detailed guidance meant that some set up a large number of small ACPs and others, particularly in built-up areas, opted for a smaller number of large ACPs.
On average, PCTs set up 14 ACPs to allow 'flu friends' to collect antivirals.
But there was a 55-fold difference across PCTs in the number of people covered by each ACP, from around 5,400 to 295,000.