A government official said that those arrested included men from Lashkar-e-Islam, a Pakistan-based tribal group that denies links to the Taliban.
The statement said that local populations have received the operation positively.
But Sohail Rahman, Al Jazeera's correspondent in Peshawar, reported that there was opposition to the operation in the region, particularly from those whose livelihoods have been hit.
Mohammed Yousef, the owner of a match factory, which employs more than 200 workers and borders the Khyber agency, said that his business had been badly affected.
"A lot of our employees had trouble getting into the factory for work, so we faced worker shortages. It affected our production," he said.
Youssef said that reports of the operation stopped potential international customers from visiting the factory and signing deals.
Haji Muhammed Asif, president of the chamber of commerce and industry in Peshawar, told Al Jazeera that a prolonged offensive would damage the economy.
"Everyone was very keen to invest in this area. But when they ask one question about the law and order naturally we had no answer," Asif said.
"The existing industrialists and businessmen are disinvesting at the moment."
About 100 college students also protested against the operation on Wednesday, officials and witnesses said.
They believe that the US have encouraged Pakistan to launch the action and want it to be stopped as they think it will cause food shortages.
But the Pakistani government ministers say the operation is needed to install law and order so that investors will come to the region.
Richard Boucher, the US assistant secretary of state, when visiting Islamabad on Wednesday also said that the military action was "very welcome".