The ministry says the new cell is led by a Palestinian and includes 24 Egyptians, mostly engineers and technicians, and it had contacts with militants in the Gaza Strip as well.
"They believe in takfiri and jihadi thought," the statement said, referring to the radical Sunni Muslim ideology espoused by militant groups like al-Qaida.
The group planned to use explosives rigged with mobile phone-activated detonators against shipping in the busy Suez Canal, and learned about explosives from al-Qaida militants on jihadi Web sites, said the statement.
In April, Egypt announced it had disrupted a militant cell linked to Lebanon's Shiite Hezbollah movement which also planned to target the Suez Canal.
One of the suspects in Thursday's case also crossed into Gaza Strip to meet up with the Palestinian Army of Islam group to receive instructions on attacking vital and important targets in Egypt, the ministry added.
A group by that name did once operate in Gaza, but was later dismantled by the local Hamas rulers.
Authorities confiscated explosives, diving suites, and electronics, as well as a handgun linked to an attack on a Coptic Christian's jewelry shop in May 2008.
According to the confessions, the detainees killed the Copt and his three workers during a robbery. They also received funds from Islamic charities abroad.
In May, Egypt announced arrests of seven alleged members of the same Palestinian Army of Islam for the bombing in February at Cairo's Khan el-Khalili bazaar that killed one French woman.
Diaa Rashwan, expert in Islamic militant groups, expressed skepticism and said there are many question marks surrounding the Interior Ministry's allegations, and similar cases had never gone to court.
"Here is a catalog of accusations, targets and ties to different groups that don't fit together," Rashwan said.
In Lebanon, meanwhile, a military court convicted 12 Palestinians, also described as inspired by al-Qaida, of committing terrorist attacks. Five of them were sentenced in absentia and given life in prison.
All the defendants, mostly Palestinians, were members of the militant Fatah Islam group which battled Lebanese troops for three months in northern Lebanon in 2007. The 12 were found guilty of carrying out bomb attacks in the north and south of the country and establishing an armed gang with the aim of attacking people and weakening state authority.