Demonstrators in multiple Turkish cities took to the streets following his arrest earlier this week.
Interior Minister Ali Yerlikaya posted on social media that 343 suspects had been detained in protests in major cities on Friday night.
"There will be no tolerance for those who seek to violate societal order, threaten the people's peace and security, and pursue chaos and provocation," Yerlikaya said.
The cities listed included Istanbul, Ankara, Izmir, Adana, Antalya, Canakkale, Eskisehir, Konya and Edirne.
The mayor, who is a popular opposition figure and seen as a top challenger to President Recep Tayyip Erdogan, was detained on Wednesday following a dawn raid on his residence over allegations of financial crimes and links to Kurdish militants.
Dozens of other prominent figures, including two district mayors, were also detained.
Many view the arrest as a politically driven attempt to remove a popular opposition figure and key challenger to Erdogan in the next presidential race, scheduled for 2028.
Government officials reject accusations that legal actions against opposition figures are politically motivated and insist that Turkey's courts operate independently.
On Saturday, police questioned Imamoglu for some five hours as part of an investigation into allegations of aiding the outlawed Kurdistan Workers' Party, or PKK, the Cumhuriyet newspaper reported.
A day earlier he was questioned for four hours over the corruption accusations.
The mayor rejected all charges during both interrogations.
He was expected to be transferred to a courthouse later on Saturday for questioning by prosecutors and to face possible charges.
His arrest has ignited protests that have steadily increased in intensity.
On Friday, police in Istanbul used pepper spray, tear gas and rubber bullets to push back hundreds of protesters who tried to break through a barricade in front of the city's historical aqueduct while hurling flares, stones and other objects at officers.
Police also dispersed groups that had rallied outside of the city hall for a third night after the opposition Republican People's Party leader, Ozgur Ozel, delivered a speech in support of the mayor.
Simultaneously, police broke up demonstrations in Ankara, the capital, as well as in the coastal city of Izmir.
Thousands marched in several other cities calling on the government to resign.
Earlier, Erdogan said the government would not tolerate street protests and accused the opposition party of links to corruption and terrorist organisations.
Authorities in Ankara and Izmir, meanwhile, announced a five-day ban on demonstrations following a similar measure imposed earlier in Istanbul.
Imamoglu's arrest came just days before he was expected to be nominated as the opposition Republican People's Party's presidential candidate in a primary on Sunday.
Ozel has said the primary will go ahead as planned.
The opposition party has also urged citizens to take part in a symbolic election on Sunday - through improvised ballot boxes to be set up across Turkey - to show solidarity with Imamoglu.
In a message on his social media account on Saturday, Imamoglu called his arrest a "coup" and accused the government of exploiting the judiciary and worsening the country's troubled economy.
"With your support, we will first defeat this coup, and then we will send packing those who caused this," he wrote on X.
