The federal government will hand-out thousands of rapid test kits for syphilis to counter an epidemic of the sexually transmitted disease in rural communities.

Erasing a syphilis epidemic sweeping indigenous communities will not only require the distribution of rapid test kits but also ending the shame associated with the disease, a leading sexual health physician says.

The federal government will distribute on Monday, as part of an $8.8 million plan to tackle the outbreak, more than 60,000 rapid test kits across Townsville, Cairns and Darwin.

Cairns Sexual Health Service physician Dr Darren Russell, who is also an associate professor at James Cook University, says the kits were "long overdue" but only part of the solution.

Since 2011, more than 1000 cases had been recorded in north Queensland including 11 babies with congenital syphilis of which six have died.

"We've had an epidemic in Queensland ... and that has spread across to the Northern Territory, Western Australia and more recently South Australia," he said.

"It's nearly all in Aboriginal and Torres Strait Islander people and that is who this initiative is aimed at."

There is not a lot of awareness in young people generally, whether they are indigenous or not, about sexually transmitted diseases, Dr Russell said, adding there is also a lot of shame (associated with it).

"We have to tackle it from all of areas and including the shame and education."

Federal Indigenous Health Minister Ken Wyatt said the strategy included upskilling, boosting the number of health workers and developing culturally-appropriate education material.

"This is a test-and-treat model involving the use of rapid Point-of-Care Tests and same-time treatment of positive cases, plus a special focus on pregnant mothers," Mr Wyatt said in a statement.

Mr Russell says he has been using the rapid test kits in his Cairns clinic since 2013 and once a finger-prick of blood is obtained it takes just 10 minutes to achieve the result.

It takes one injection of penicillin to treat an early case of syphilis and babies are treated intravenously, he said.

"We don't get lasting immunity to it. You can get it again."

Early signs of syphilis arise within nine to 90 days after contact with a person and it presents as a sore or an ulcer, which is know as a chancre, usually on the genitals," he said.