After evading queries on the number of deaths, Mishra conceded yesterday that 44 persons have succumbed to the infection this year.
Led by the Congress corporator Monu Saxena, protesters were prevented by police from reaching the minister's residence in Char Imli area.
Saxena also demanded sacking of Principal Secretary, Health, Pravir Krishna on the issue.
He also alleged irregularity in purchasing of drugs including for swine flu and said the medicines were fake and unable to check the spread of H1N1 virus in the state.
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AAP workers held a demonstration in front of Mishra's residence and demanded his resignation over the issue, saying the reins of Health department be handed over to a "competent" minister.
AAP's state secretary Akshay Hunka and party leader Paras Saklecha said more than 200 people have succumbed to the dreaded virus in the state but the state government is not admitting the same and has revealed the figures of deaths in urban areas only.
The AAP leaders also demanded a compensation of Rs 5 lakh each to the kin of the deceased and a government job to a member of his/her family.
He asked authorities concerned to ensure that all hospitals have adequate arrangements to deal with the situation.
Singh said there was no shortage of medicines and other facilities and all such amenities are also being provided to government authorised private hospitals.
The chief minister also reviewed the situation at the Mantralaya today along with health minister and senior health department officials.
Chouhan also spoke to Union Health Minister J P Nadda on the issue, an official at the Mantralaya said.