The wasted medicines were combination of different vaccines and were used to immunise children against tetanus, diphtheria, whooping cough, Hepatitis B, meningitis and pneumonia.
Minister of state for National Health Services Saira Afzal Tarar said that some official have been suspended and a probe has been launched to find if more people were involved.
Tarar said the vaccines were ruined because of "departmental conflicts".
However, an official of Health Ministry said that the frequent power outage was the main cause of the loss as top bosses failed to address the problem despite complaints by lower staff.
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The scandal is the latest problem to be exposed in Pakistan's poorly run public health services.
Immunisation of children is a major issue in Pakistan, specially for polio. Last year, 306 cases of polio was reported in the country, the highest in 14 years. At least nine cases have been detected so far.
Militant groups often attack polio teams as they see vaccination campaigns a cover for espionage. There are also long running rumours about polio drops causing infertility.
Yesterday in Peshawar police arrested 471 parents who refused to administer polio vaccine to their children during the ongoing two-day anti-polio campaign.