The pentavalent vaccines, which protect against five diseases with a single shot, spoiled because they were not stored at the proper temperature, officials said.
Read: Pakistan wastes $3.7 million worth of donated vaccine, official says
"An inquiry commission was formed to investigate the case and has suspended two officials for negligence," Dr Saqlain Ahmad Gilani, the national manager at the Expanded Programme on Immunisation told AFP.
"The vaccines were stored on a higher temperature than required."
The vaccines worth $3.7 million were donated by the United Nations Children's Fund (UNICEF), he said.
State minister of National Health Services Regulation and Coordination Saira Afzal Tarar confirmed the incident and said it would lead to an improvement in vaccine monitoring.
Read: At their peril: Over 450 parents held for refusing polio drops
Tarar said the vaccines were ruined because of "departmental conflicts".
"It appears that one person was switching off the generator when it was turned on apparently to save fuel," she said.
She said the inquiry report will be finalised in a week and made public and insisted more than half of the vaccines could still be used.
The pentavalent vaccine does not cover polio.
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