Pakistan recorded 72 cases of polio this year compared to 58 for all of 2012, a World Health Organisation (WHO)official said on Wednesday.
Pakistan is one of only three countries in the world where the highly infectious crippling disease remains endemic.
But opposition from militant groups has hampered efforts to immunise children, with vaccination teams murdered in some cases.
Officials said the violence and suspicions about the vaccine were the reason for the increase in cases.
"Pakistan has reported 72 polio cases which is highest in comparison to two other countries with the disease, as Nigeria has 50 cases and Afghanistan reported only nine during 2013," Elias Durry, emergency coordinator for the WHO's Polio Eradication Pakistan Program, told reporters.
According to a global update for polio cases, Pakistan had 58 cases last year while Nigeria had 110 and Afghanistan 31.
Six cases this year have been reported in the eastern province of Punjab, six in Sindh in the south and 10 in northwestern Khyber Pakhtunkhwa.
But by far the bulk of the infections—50—were in the lawless tribal areas along the Afghan border.
The Pakistani Taliban banned polio vaccinations in the tribal region of Waziristan last year, alleging the campaign was a cover for espionage.
"We successfully immunised over 33 million children during the recent vaccination campaign while 2.3 million children were recorded missed during the campaign," Durry said.
He said that in most cases children were missed in the areas where the law and order situation was not favourable, and where vaccination teams faced security threats.
More than 47,000 children missed vaccination because of parental refusals.
In August health officials warned of the danger of a serious polio outbreak in the northwest, saying more than 240,000 children had missed vaccination because of the Taliban ban.
Elsewhere in the country, health workers giving out polio drops have been attacked and killed, including in the largest city Karachi.
Polio cases reached a low of 28 in 2005 but rose to 198 in 2011.
Last month, the WHO linked an outbreak of polio in Syria that has paralysed 13 children to a strain of the virus from Pakistan.