Police fired live ammunition and tear gas to quell the riots, killing two people, he said.
There was no immediate claim of responsibility for the attack.
The bombing, which also wounded 35 people, and clashes raised fears of wider Hindu-Muslim violence in the city, long-plagued by communal tensions and occasional spasms of inter-religious bloodletting.
Authorities across India were told to be alert for any signs of Hindu-Muslim fighting and top officials called for calm.
Many of the 35 people wounded were seriously hurt, and the city's police chief, Balwinder Singh, warned the death toll could rise.
Y. S. Rajasekhara Reddy, chief minister of Andhra Pradesh state, appealed for calm between Hindus and Muslims.
He called the bombing an act of "intentional sabotage on the peace and tranquility in the country."
Prime Minister Manmohan Singh echoed those sentiments in a statement released later.
"The prime minister has condemned the bomb blast in Hyderabad and has urged members of all communities to maintain peace and communal harmony," his media adviser, Sanjaya Baru, said in the statement.
Reddy told reporters in New Delhi, where he was meeting with federal officials on unrelated business, that one bomb went off around 1:30 p.m. and that police found and defused two other bombs soon after.
About 10,000 people usually attend Friday prayers at the mosque, which is in a Muslim neighborhood of Hyderabad, and the blast sparked a panic.
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