The regulator's chief executive, Mick Aldridge, wrote a letter to Cambridgeshire chief constable Julie Spence, who is the head of the Association of Chief Police Officers' Citizen Focus business area.
In the letter Aldridge raised his concerns about a number of incidents in which police have used "insensitive efforts" to check street fundraisers' credentials.
The letter accused some police of focusing "disproportionate attention" on high-street fundraisers, and recounted incidents in which conversations between chuggers and members of the public were interrupted by officers.
Spence asked her ACPO colleagues to highlight the PFRA's concerns to their police forces and "encourage a sensitive, diplomatic and proportionate approach where charity representatives need to be engaged".
Aldridge said: "It would be wrong to suggest that heavy-handed policing has been a widespread problem for PFRA members but there had been enough such instances to cause us concern and it was something that we hoped we could nip in the bud."
The letter has been well received by the police and led to a sergeant from Surrey Constabulary contacting the PFRA and offering to act as a liaison officer.
Aldridge said: "ACPO have been incredibly co-operative and I have no doubt this intervention will go a long way to ensuring a much smoother relationship with neighbourhood policing teams."
ACPO advised the PFRA that face-to-face fundraiser teams contact local police before visiting areas, a recommendation the PFRA said it is happy to endorse.