The operation came just a day after at least 23 soldiers were killed in a Daesh attack that targeted two military checkpoints in the region.
Egyptian police officers have shot dead 16 gunmen in two shootouts, the country's Interior Ministry said on Saturday.
It said that most of those killed were fugitive militants linked to recent attacks on security forces in Northern Sinai.
Egypt faces an insurgency led by Daesh in the restive Sinai Peninsula, where hundreds of soldiers and police have been killed since 2013.
At least two policemen were killed and nine wounded when their armoured vehicle was hit by an explosion in the Sinai on Saturday, Egypt's state news agency MENA said.
Saturday's attack came a day after at least 23 soldiers were killed when suicide car bombs tore through two military checkpoints in the region in an attack claimed by Daesh. It was one of the bloodiest assaults on security forces in years.
The Interior Ministry said that gunmen had opened fire on police as they approached a desert training camp for militants in Ismailia. The officers returned fire, killing 14 militants, five of whom have been identified so far.
The camp was used to "subject (recruits) to military training programmes on the use of various types of firearms and manufacture explosive devices...," the ministry said in a statement.
In a separate statement the ministry also said its forces killed two men described as fugitive terrorists in an exchange of gunfire in the city of Giza.
The men, who were inside an apartment, opened fire on security forces as soon as the officers approached to arrest them, it said.
The ministry said the pair were members of a newly emerged militant group called Hasm, which claimed responsibility for the killing of a homeland security officer outside his home in Qalubiya, a province just north of Cairo, while on his way to prayers on Friday.
Hasm has claimed several attacks around Cairo targeting judges and policemen since last year.
Other militant groups such as Hasm, which the government says are linked to the Muslim Brotherhood, are active in Cairo and other cities where they have targeted security forces, judges and pro-government figures.
The Brotherhood was outlawed in 2013 after the military ousted one of its leaders, Mohamed Mursi, from the presidency following mass protests. It maintains that it is a peaceful organisation.
Daesh has also intensified attacks on security forces and Coptic Christian civilians in the mainland in recent months, killing about 100 Copts since December.