The requirement for GPs to take samples from suspected cases also stretched resources of the regional health protection units expected to co-ordinate this work.
In some areas, the workload involved in containment was unsustainable and testing could not be continued, the HPA said.
The report points out that the UK's approach to containment, which included testing of cases and provision of prophylaxis to patients and close contacts, was intended to slow the spread of infection and buy time.
It concludes that the impact of containment 'is likely to have been small'. 'It is also possible that the containment measures during this period had no effect on the course of the pandemic,' the report adds.
Comprehensive containment would 'inevitably' have been difficult to achieve for a variety of reasons, the HPA said.
Infection may have already been spreading readily before containment measures began. In addition, the virus was brought into the country repeatedly from different areas overseas and newly imported cases were not detected fast enough.
Also, prophylaxis was not used in many cases because mild symptoms meant patients did not seek medical advice, and delays in providing prophylaxis led to onward transmission.
The report suggests that the limitations of the containment strategy, and need to move to a treatment phase, could have been recognised almost two months before the DoH decided to abandon it.
'From June there was increasing evidence of transmission in the wider community,' the HPA said. 'This suggested a containment approach would not be effective. Arguably, it should have been stopped at this time to be replaced by a treatment-only approach.'