Unrest in northwestern Swat and tribal areas bordering Afghanistan have hindered anti-polio vaccination teams from reaching a large number of children.
The first of the latest cases was confirmed in Nawagai village in restive Bajaur tribal district in a 16-month-old boy, and the second was detected in a 10-month-old boy in southwestern Baluchistan.
"A case of P3 polio virus has been confirmed in Nawagai. The parents had refused to give vaccination drops to their son," district support officer Hameedur Rehman told reporters.
Bajaur is one of seven Pakistani tribal areas where many locals believe polio vaccinations are intended to reduce the Muslim population. P3 polio is less contagious and dangerous than the crippling P1 and P2 types.
Authorities confirmed that the second case in Ragoor village in Baluchistan, which borders Afghanistan and Iran, was the P1 type.
"We have really been alarmed by this case since we were hoping to make the province and the country polio free," district health official doctor Rehmat Ullah told AFP.
Ullah said a regular vaccination drive was progressing well in the area on Tuesday.
But officials said polio vaccination teams in northwestern Swat valley were stopped Tuesday and some of the health workers were beaten up. Two polio cases were detected in that area earlier this month.
The World Health Organisation recently listed Nigeria, India, Pakistan and Afghanistan as the only countries in the world where polio is endemic.