Mr O'Connor drew attention to the issue in a recent column in the association's magazine, writing that the Government had demanded that not only reported crime be reduced, but also the number of prosecutions.
"Combine that with a change in emphasis from police being absolutely victim-focused and you have a significant change in the way police work."
Officers were being criticised by the Independent Police Conduct Authority and coroners who had reconstructed cases and found that police should have prosecuted, regardless of a victim's wishes, Mr O'Connor said. He included the recent Roast Busters case as an example.
Police Minister Michael Woodhouse said the Police Association was "completely incorrect".
"There's no doubt police are committed to reducing reported crime and that is entirely consistent with their Prevention First strategy. But any suggestion of government influence over recording crime or decisions to prosecute are simply without foundation," he said.
Non-traffic prosecutions have fallen by 41 per cent from 2008/09 to 2013/14. A police spokesman said that was in line with the overall drop in crime and the adoption of alternative resolutions such as pre-charge warnings and community justice panels.
From the introduction of pre-charge warnings in September 2010 to June last year, 74,264 such warnings were used - allowing officers to arrest a person, take them for processing and then issue a warning as an alternative to prosecution.
"More than half the offences resolved with a pre-charge warning are generally disorder or breach of liquor ban offences," the police spokesman said.
A policing excellence strategy, which was launched in August 2010, had targets including a 19 per cent reduction in non-traffic prosecutions.
The overhaul was in response to pressures including funding and increases in workload, and aimed to fundamentally change the way police operate.
A police spokesman said policing excellence was police and not Government-initiated.
• The police have targeted a drop in prosecutions as well as recorded crime, and non-traffic prosecutions have fallen by 41 per cent from 2008/09 to 2013/14.
• The police association says it is not opposed to the new approach, but has warned that members are being criticised about cases where no prosecution was brought, and that the prospect of court is a powerful deterrent for some.