Mered Medhanie, dubbed The General, is said to be the mastermind of an international smuggling network who is responsible for the deaths of hundreds of migrants in the Mediterranean.
The 35-year-old Eritrean, who earned the nickname because he styled himself on former Libyan dictator Muammar Gaddafi, was arrested in the Sudanese capital Khartoum in May before being extradited to Italy on Tuesday.
They said the man sent to Italy was in fact Medhanie Tesfamariam Kidane, a 27-year-old refugee arrested in a street in Khartoum late last month, the newspaper said.
An NCA spokesman said: “We have noted the Guardian’s report. This is a complex multi partner operation and it is too soon to speculate about these claims.”
It is thought Medhanie ran an empire smuggling thousands of migrants from Africa and the Middle East into Europe by regular journeys across the Mediterranean.
Tom Dowdall, NCA deputy director, said earlier: “Medhanie is a prolific people-smuggler and has absolute disregard for human life.
“Although he was operating thousands of miles away, his criminal activity was impacting the UK. Medhanie no doubt thought he was beyond the reach of European justice but we were able to support the Italians by tracking him down to Sudan.”
According to Italian prosecutors Medhanie was responsible for the death of 359 migrants who drowned after their boat sank off the Italian island of Lampedusa in 2013.
In an intercepted conversation he could be heard laughing about the fatal overloading of migrant ships.
In other recordings he discussed organising journeys across the Mediterranean and co-ordinating smuggling gangs.
Operation Glauco, a probe set up by the Italian authorities in the wake of the Lampedusa tragedy, was assisted by NCA officers from the UK Immigration Crime Taskforce in tracking down the kingpin to an address in the El Diem area of Khartoum.
GCHQ assisted the NCA in trawling through chatter, while the agency used its “international network” to set up a trap with Sudanese authorities. Medhanie was arrested by the Sudanese National Police on 24 May.
He is charged with being the organiser of a transnational criminal conspiracy aimed at smuggling human beings from Africa to Italy, and on to northern Europe and the UK.
Other charges include the smuggling of migrants relating to numerous arrivals of boats in Sicily, with aggravating circumstances of the number of smuggled people, inhuman treatment and risk to the life of migrants.