Both new cases are from northwestern region, including one each from Khyber-Pakhtunkhwa province and tribal areas, which is directly controlled by the federal government.
An official form the National Institute of Health (NIH) in Islamabad confirmed the new cases.
The official said that 16-month-old Salma belongs to Khyber tribal region while 8-month-old Habiba is resident of a suburban area of provincial capital Peshawar.
Peshawar has been dubbed as hub of poliovirus which authorities have failed to eradicate despite several anti-polio campaigns.
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So far, 119 cases have been reported from tribal areas this year. Another 28 surfaced in Khyber Pakhtunkhwa, 14 in Sindh, three in Balochistan and two in Punjab.
In 2012, 58 polio cases were recorded which increased to 93 in 2013.
Pakistan, which is already facing travel restrictions imposed by the World Health Organisation, is among the three countries along with Nigeria and Afghanistan where polio virus is endemic.