The virus was detected in the sewage samples of Peshawar and Bannu cities of KP, and Punjab’s capital Lahore, the Ministry told Xinhua news agency.
It said that the environmental samples were taken from 70 sites across the country.
A few days ago, the virus was found in the samples from Rawalpindi, Sialkot and Bahawalpur cities of Punjab, the Ministry said.
Wild polio-I has been detected in 17 environmental samples this year.
However, the scale of its presence all over the country could not be found due to monsoon rains and floods in Sindh and Balochistan provinces, according to the Ministry.
Pakistan had a polio-free run for almost a year but 14 new cases, all from the violence-stricken province, have been reported in so far this year.
Pakistan is one of the few countries in the world where new polio cases still surface, though the number of affected children has declined massively compared to 306 in 2014.
Neighbouring Afghanistan also has a similar problem, with the UK and US both recently recording polio in waste water.
Militants linked to Al Qaeda often attack health workers in Pakistan.
Dozens of vaccine handlers and security officials have been killed in the past.
IANS