Also, almost all the new cases were in the southern provinces, which see the worst of a deadly Taliban rebel-linked insurgency, with the insecurity hampering efforts to wipe out the crippling disease.
"We have 13 cases since the beginning of this year," Health Minister Mohammad Amin Fatimie told an event to mark the start of a new round of polio vaccinations.
Most of the cases were in children aged under two years, he said. The number was down from 31 in 2006 and 17 in 2007.
"The first challenge is that the immunization teams are not able to cover every single house and the enemies of Afghanistan are stopping the process," Fatimie said, referring to Taliban and other militants.
There are large parts of mainly southern Afghanistan that are considered dangerous, even for Afghans, with insurgents and other rebels kidnapping and sometimes killing people associated with the government.
Nineteen non-government organization workers have been killed this year, according to an umbrella body of NGOs, the Agency Coordinating Body for Afghan Relief.
In some cases Taliban were speaking out against the vaccination campaign and telling people not to participate, the health minister said.
"The second challenge is one of the four countries that have polio is a neighboring country, Pakistan," he said.
Hundreds of people move every day between Afghanistan and Pakistan, where there have been 20 cases of polio this year, and this spreads infection.
"Our coverage is 90 percent in insecure areas and in the areas that there is active fighting or the area is battlefield or there is danger from mines -- they are necessarily out of coverage," ministry spokesman Abdullah Fahim said.
The ministry said the three-day immunization drive starting Sunday would see more than 52,000 staff and volunteers deliver oral polio vaccinations to 7.5 million children across the country.