The aim of the new programme is to reduce the number of Manx women who develop cervical cancer.
The additional test would mean more focussed treatment for "higher risk" individuals.
A spokesman said abnormalities caused by HPV can easily be treated before becoming dangerous.
He added: "With the discovery that HPV causes the majority of cervical cancers and following research and trials over many years, it is now possible to screen for high risk HPV as part of the existing cervical screening programme.
The test for high risk HPV is done on the cervical screening sample, which means that women will not notice anything different when they have their regular cervical smear test.
All women in the Isle of Man between the ages of 25 and 49 are called for cervical screening every three years.
Those between 50 and 64 are called every five years.

It appears to tell a simple story from an American high school, but also has a hidden meaning revealed at the end.
The unexpected message has propelled the short film to more than two and a half million views on YouTube in just three days.
Spoilers follow below - you may want to watch the video to the end first.
It was created by the Sandy Hook Promise group, set up by family members of the victims of the Sandy Hook school shooting.
On December 14, 2012, 20 children and six adults were killed at Sandy Hook Elementary School by 20-year-old Adam Lanza, who had killed his own mother earlier that morning. He was a former student of the school.
"When you don't know what to look for or can't recognize what you are seeing, it can be easy to miss warning signs or dismiss them as unimportant," said Nicole Hockley from Sandy Hook Promise, whose son Dylan died in the shooting.
"Everyone has the power to intervene and get help. These actions can save lives."
In the aftermath of the 2012 shooting, Barack Obama called for action on gun control, despite the political difficulties.
But three years later, he called gun control the greatest frustration of his presidency, as the US Congress repeatedly blocked moves to tighten restrictions.
The gun control movement reached a peak in the summer when more than 200 Democratic politicians staged a sit-in at the House of Representatives to demand a vote on restricting firearm purchases, in the wake of the Pulse nightclub shooting in Florida.
The Gun Violence Archive non-profit organisation maintains a "mass shooting tracker" of attacks where four or more people were shot in a single incident.
It estimates that so far in 2016, 425 people have been killed in 362 mass shootings in the United States. It says there were 333 mass shootings last year, and 275 two years ago.
The new President-elect Donald Trump, however, frequently expressed support for the second amendment - the right to bear arms - during his campaign, saying his rival Hilary Clinton wanted to abolish it.
On one occasion, he caused a significant controversy when he suggested gun rights supporters could somehow stop Ms Clinton's campaign.
In May, the National Rifle Association, a pro-gun lobby, endorsed Mr Trump for president.
A test for the Human Papilloma Virus (HPV) is to be included within the Isle of Man's cervical cancer screening programme, says the health department.
[NEXT_CONCEPT]
A video telling the story of two schoolchildren forming a friendship - with a twist - has gone viral online.