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The explosion shattered the windows of the red and black bus as it passed near a busy intersection in the capital's northern neighbourhood of Nasr City.
Police defused a second bomb at the site and cordoned off the area as sniffer dogs searched for more explosive devices, an AFP correspondent said.
The bombing came a day after the military-installed government declared Morsi's Muslim Brotherhood a terrorist organisation and a suicide car bomber killed 15 people at a police headquarters north of Cairo on Tuesday.
The interior ministry said that attack was meant to intimidate voters ahead of a referendum next month on a new constitution, billed as the first step in a democratic transition ahead of parliamentary and presidential elections.
On Thursday, Egyptian prosecutors ordered at least 18 Muslim Brotherhood members, including an ex-lawmaker, held on accusations of belonging to a terrorist group, state media reported.
Police also arrested 16 suspected Muslim Brotherhood members for passing out leaflets in support of the group and "inciting the violence," the official MENA news agency said.
The Brotherhood's designation as a terrorist group means anyone joining their rallies could be jailed for five years, while those possessing their literature or supporting them "verbally or in writing" could face up to five years, a ministry statement said.
The Brotherhood still organises almost daily protests demanding Morsi's return almost six months after the military overthrew him.
More than 1,000 people have been killed in street clashes and thousands imprisoned in a police crackdown on the movement since Morsi was ousted on July 3.
Sisi, who led the ouster of Morsi, vowed to fight terrorism in the deeply polarised country.
"Do not allow these terrorist actions to affect you," the army quoted him as saying at a military ceremony.
"If you want freedom and stability, which is not achieved easily, then you have to trust God and your army and your police."
Following Thursday's blast in Nasr City, police General Mohamed Gamal showed reporters a defused pipe bomb he said had been placed inside a nearby advertising display and primed to explode when police arrived at the scene.
"It was set to go off remotely," interior ministry spokesman Hany Abdel Latif told AFP, adding the bombs were "meant to terrorise people before the referendum."
'My country is bleeding'
A witness described scenes of panic after the attack .
"I was 100 metres (yards) away when I heard the explosion. I came running to help the wounded," said Mahmud Abd al-Al, a construction worker.
"They were covered in blood. One man lost a leg," he said.
Dozens of angry men and women chanted slogans against the Muslim Brotherhood as police tried to keep them away from the site of the blast while forensic experts searched for clues inside the bus.
"The Muslim Brotherhood people are dogs," chanted 40-year-old Fadiya as police pushed her away.
"My country is bleeding. Everybody is scared now in Egypt, even the police are scared," she said as some took pictures of the targeted bus with their mobile phones.
Residents of Cairo expressed fear on Thursday.
"This is not the city I used to know," said taxi driver Ihab Abdelmoneim commenting on the attack.
"Today, I am scared of the passenger who sits in my taxi and he is scared of me."
The Brotherhood, which won all elections since the 2011 ouster of Hosni Mubarak, insists it is peaceful and has condemned militant attacks.
The authorities also shut down the newspaper run by the Freedom and Justice Party, the political wing of the Islamist group, and seized several presses belonging to the movement, the interior ministry said.
The deadliest attacks, including Tuesday's bombing, have been claimed by the Al-Qaeda-inspired Ansar Beit al-Maqdis group based in the restive Sinai.
The group, composed mostly of Egyptian Bedouin, has criticised the Brotherhood's style of political Islam and advocates armed attacks.
Authorities say there are links between the Sinai jihadists and the more moderate Brotherhood, but have offered no proof.
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Police defused a second bomb at the site and cordoned off the area as sniffer dogs searched for more explosive devices, an AFP correspondent said.
The bombing came a day after the military-installed government declared Morsi's Muslim Brotherhood a terrorist organisation and a suicide car bomber killed 15 people at a police headquarters north of Cairo on Tuesday.
The interior ministry said that attack was meant to intimidate voters ahead of a referendum next month on a new constitution, billed as the first step in a democratic transition ahead of parliamentary and presidential elections.
On Thursday, Egyptian prosecutors ordered at least 18 Muslim Brotherhood members, including an ex-lawmaker, held on accusations of belonging to a terrorist group, state media reported.
Police also arrested 16 suspected Muslim Brotherhood members for passing out leaflets in support of the group and "inciting the violence," the official MENA news agency said.
The Brotherhood's designation as a terrorist group means anyone joining their rallies could be jailed for five years, while those possessing their literature or supporting them "verbally or in writing" could face up to five years, a ministry statement said.
The Brotherhood still organises almost daily protests demanding Morsi's return almost six months after the military overthrew him.
More than 1,000 people have been killed in street clashes and thousands imprisoned in a police crackdown on the movement since Morsi was ousted on July 3.
Sisi, who led the ouster of Morsi, vowed to fight terrorism in the deeply polarised country.
"Do not allow these terrorist actions to affect you," the army quoted him as saying at a military ceremony.
"If you want freedom and stability, which is not achieved easily, then you have to trust God and your army and your police."
Following Thursday's blast in Nasr City, police General Mohamed Gamal showed reporters a defused pipe bomb he said had been placed inside a nearby advertising display and primed to explode when police arrived at the scene.
"It was set to go off remotely," interior ministry spokesman Hany Abdel Latif told AFP, adding the bombs were "meant to terrorise people before the referendum."
'My country is bleeding'
A witness described scenes of panic after the attack .
"I was 100 metres (yards) away when I heard the explosion. I came running to help the wounded," said Mahmud Abd al-Al, a construction worker.
"They were covered in blood. One man lost a leg," he said.
Dozens of angry men and women chanted slogans against the Muslim Brotherhood as police tried to keep them away from the site of the blast while forensic experts searched for clues inside the bus.
"The Muslim Brotherhood people are dogs," chanted 40-year-old Fadiya as police pushed her away.
"My country is bleeding. Everybody is scared now in Egypt, even the police are scared," she said as some took pictures of the targeted bus with their mobile phones.
Residents of Cairo expressed fear on Thursday.
"This is not the city I used to know," said taxi driver Ihab Abdelmoneim commenting on the attack.
"Today, I am scared of the passenger who sits in my taxi and he is scared of me."
The Brotherhood, which won all elections since the 2011 ouster of Hosni Mubarak, insists it is peaceful and has condemned militant attacks.
The authorities also shut down the newspaper run by the Freedom and Justice Party, the political wing of the Islamist group, and seized several presses belonging to the movement, the interior ministry said.
The deadliest attacks, including Tuesday's bombing, have been claimed by the Al-Qaeda-inspired Ansar Beit al-Maqdis group based in the restive Sinai.
The group, composed mostly of Egyptian Bedouin, has criticised the Brotherhood's style of political Islam and advocates armed attacks.
Authorities say there are links between the Sinai jihadists and the more moderate Brotherhood, but have offered no proof.
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