According to the polio virology lab at the National Health Institute, samples of sewage water collected from Lahore and Karachi had tested positive for the virus.
The samples taken on April 12, from Lahore's Main Outfall pumping stations confirmed the presence of the polio virus.
The Prime Minister's point person on polio, Ayesha Raza Farooq, confirmed that an environmental sample from Lahore and two from Karachi have tested positive for virus, Dawn News reported.
However, Farooq said she was not "too concerned about (the environmental sample testing positive in) Lahore because there are no reported cases which means a high level of immunity has developed among the population so while the virus is still circulating it is a low-grade one".
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So far, there have been 61 reported cases of polio in Pakistan this year.
The WHO decided to impose strict travel restrictions on Pakistan to prevent the possible spread of the polio virus to other countries.
The WHO says the strain of polio virus found in Pakistan has affected as many as five countries over the past two years, becoming a serious threat to other countries.