The Pharmacy Guild of Australia has dismissed warnings from the peak body for GPs that patients should avoid health check ups at pharmacies.

Pharmacists and GPs are at loggerheads over whether patients should undergo health checks at their local chemist shops.

Dr Cameron Loy, the Victoria chair of the Royal Australian College of General Practitioners (RACGP), says patients should steer clear of having heart, diabetes and cholesterol checks at pharmacies.

He argues the only motivation for pharmacists to offer the checks is money, a claim denied by the Pharmacy Guild of Australia.

"Health checks are not comparable to buying toothpaste, hair dye or vitamins but part of the ongoing continuity of care, the long-term engagement, that general practice delivers," Dr Loy told Fairfax Media on Monday.

"These pharmacies are motivated by money, the opportunity to have more people in the store to buy other things."

But the Pharmacy Guild of Australia has accused the RACGP of acting in the self-interest of doctors who want to keep their waiting rooms full instead of accessing health checks elsewhere.

The guild's Victoria Branch president Anthony Tassone said the RACGP's claims were alarmist and undermine the good working relationship between most doctors and pharmacists.

"Community pharmacies work closely with local GPs in the interests of patients, and appropriate health checks performed in pharmacies can be an important way to identify those at risk and refer them back to their doctor - whom they may not have seen for some time," he said in a statement.

"Not everybody has a regular GP, but community pharmacies are helping refer patients to a GP every day across Australia."

However Dr Loy argues that there are long-term dangers for patients who don't have their GPs regularly review their healthcare needs and instead rely on pharmacy health checks.

"I've had patients who have done health checks somewhere else and and they've been left confused by the results because they don't make a lot of sense, they haven't been contextualised," he said.

Mr Tassone said health checks in pharmacies should always be carried out with a view to collaborating with the patient's doctor and other health professionals as required.