The Pharmacy First service, launched in January in England, extended the range of services chemists can provide, including treatment of sinusitis, earache and shingles.
Members are not being asked to pull out of the scheme, the NPA said, but a reduction in opening hours and the stopping of locally commissioned services would affect it.
The NPA says urgent funding talks with the government are needed to guarantee patient safety and services for vulnerable people.
Pharmacy funding is set by devolved governments but the medicine funding arrangements – known as the drug tariff – are decided by Westminster for pharmacies in England, Wales and Northern Ireland.
Scottish pharmacies have a separate system, and are not involved in the current ballot.
Dr Leyla Hannbeck, chief executive of the Independent Pharmacies Association, said: “The community pharmacy sector is in an escalating crisis with a £1.7 billion shortfall in its funding. This has got worse by the hike in the employers’ National Insurance, resulting in £12,000 extra costs annually for our members.
“As healthcare professionals, we believe that patients must not be caused suffering by any withdrawals of our members’ valuable and vital professional services.
“The government must urgently raise pharmacy funding to prevent further closures of community pharmacies.”
A Department of Health and Social Care spokesperson said: “Community pharmacy has a vital role to play as we move the focus of care from hospital to the community under the fundamental reforms in our 10 Year Health Plan.
“Unfortunately, we inherited a system that has been neglected for too long and is no longer supporting the pharmacists we need to deliver for patients at a local level.”
