At least 28 suspected militants have been held in Kerdasa, state TV says.
Several hours after the operation started, security forces had to take cover as clashes flared with militants.
Eleven police officers were killed at a police station in Kerdasa last month, weeks after the overthrow of Islamist President Mohamed Morsi in July.
Soldiers went into Kerdasa at about 05:30 local time (03:30 GMT) on Thursday, backed by helicopters.
State media said a senior policeman had died in clashes with militants.
Another state TV report said that one of those arrested on Thursday was Ahmad Uways, the man accused of killing the head of Kerdasa police station on 14 August.
The authorities had previously promised to respond to the deadly attack on the police station.
Egyptian security forces taking part in the operation in Kerdasa
The operation in Kerdasa began early on Thursday morning
Security forces taking cover during a gun battle with
Several hours after the operation began, gun battles with militants flared up
A military helicopter flies during clashes between security forces and suspected militants, over the town of Kerdasa
Troops were backed by helicopters in the assault
Egyptian security forces take cover
Security forces had to take cover behind buildings
Security forces and photographer
Photographers at the scene were also sent looking for cover
Reporting from the centre of the town, the BBC's Quentin Sommerville said security forces had exchanged fire with unidentified gunmen who appeared to have taken up positions in a number of buildings in the town.
Security forces had to take cover behind buildings, our correspondent added.
By Thursday afternoon, the gunfire had become less frequent but there was still a heavy police presence on the streets and and army checkpoints at all main exits, he added.
Earlier, residents had told the BBC that security forces were searching homes in Kerdasa for members of Mr Morsi's Muslim Brotherhood movement.
'Down with Sisi'
In the hours before police and soldiers moved in, the mood in the town was defiant, our correspondent says.
Thousands of people attended a pro-Morsi rally on Wednesday night amid shouts of "Down with Sisi", referring to the head of the army.
After performing dawn prayers on Thursday, troops began taking their positions in armoured vehicles ready for the start of the operation, state-run news agency Mena reported.
Military roadblocks outside Kerdasa prevented people from entering the area, our correspondent says. "I can't be responsible if you get shot," an officer was heard telling a local man.
An Egyptian man walks past a torched and vandalised police station on 24 August, 2013 in the Kerdasa neighbourhood of Giza, on the outskirts of Cairo, that was attacked on 14 August
Eleven police officers died when this police station was set on fire last month
In a separate incident on Thursday, several metro lines in the capital were disrupted after two suspected bombs were found on the tracks near Hilmiyat al-Zaytun station in the south of Cairo.
Security officials said bomb experts had been dispatched to the scene and services were now running again.
However, there was confusion as to whether the bombs were viable devices or fakes.
'Outsiders'
At least 1,000 people - including about 100 police officers - have died in unrest following President Morsi's removal from power.
The deadliest incidents took place when security forces moved in to disperse two pro-Morsi sit-ins in Cairo last month.
Kerdasa, known for producing and selling textiles, is 14km (8.7 miles) from Cairo.
Residents were quoted on Wednesday saying they did not trust police: "We know they will come to arrest people we know and respect, whom they blame for the violence that we know was done by outsiders, not by our respectable sheikhs," Ahmed Aly told Reuters news agency.
"Eleven policemen were killed here, but so too were 11 people from Kerdasa killed at Rabaa," another resident told the BBC, referring to one of the pro-Morsi camps in Cairo cleared by the police.
Pictures of Mr Morsi are still in evidence on many buildings and lampposts in the town, our correspondent reports, leaving little doubt over where many people's allegiances lie.
On Monday, Egyptian forces arrested dozens of residents during a raid on pro-Morsi supporters in the town of Delga, Minya province, about 300km south of Cairo.
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