While there were 4375 cases of VTE, further analysis of 889 women who were administered Gardasil during the study did not find a link between clots and the drug.
The observations were based on their health in the 42 days immediately following the vaccination, which is considered the main risk period.
The study's authors also factored in whether the women used oral contraceptives and blood-thinning anticoagulants.
Previous diagnoses of VTE not related to pregnancy, surgery, or cancer were also considered.
"Our results do not provide support for an increased risk of VTE following quadrivalent HPV vaccination," Nikolai Madrid Scheller and others wrote in the study published in the Journal of the American Medical Association (JAMA) on Wednesday.
"This study provides even more evidence that HPV vaccination is very safe. Early American studies, which were based on reports coming in from people who were vaccinated, had suggested that there may be an increased chance of blood clots occurring after HPV vaccination," Dr Julia Brotherton, the medical director of Australia's National HPV Vaccination Program Register, said.
"This large study based on five years of vaccination in the Danish population very elegantly analyses this issue and robustly refutes the presence of any association between HPV vaccination and blood clots.
"We can now feel very confident in stating that the HPV vaccine is very safe, having been given to around 200 million women worldwide and monitored throughout the world for side effects. Australian parents can continue to support the vaccination of their daughters and sons through our world leading HPV vaccination program with confidence."
Michael Quinn, professor of gynaecology and gynaecologic oncology at the University of Melbourne, concurred.
"This is good news for women and good news for their doctors," Professor Quinn said.
"HPV vaccination has been halted in some countries like Japan because of anxiety about side effects. These results are very reassuring and in keeping with the WHO on this vaccine's safety."
- AAP