In addition to the 300 people detained in the US so far, a string of arrests have been made in European countries, including Britain, France, Spain, Belgium, Bosnia, Ireland and the Netherlands.
The three were friends, all trained as pilots in the United States and, through Mohammed Atta, had an apparent connection to Osama Bin Laden's al-Qaeda organisation, which the US holds responsible for the attacks.
More suspects sought
Investigators believe the suspects may have shuttled between the US and Germany planning the attacks over a three year period.
They are also hunting three other men - Ramzi Binalshibh, a Yemeni national, Said Bahaji, a German Moroccan and Zakariya Essabar, a Moroccan national.
They are believed to have helped with the logistics and planning of the attacks, arranging visas, passports and other documentation, allowing the main hijack team to concentrate on flight training.
"Their connections to the hijackers are extensive ... it is clear that Hamburg served as a central base of operations for these six individuals," US Attorney General John Ashcroft has said.
In another development, German prosecutors say a Turkish man arrested in Frankfurt last week had connections to an extremist Islamic group planning terrorist attacks.
Harun Aydin, aged 29, was detained at the airport after boarding a Tehran-bound flight. His checked-in luggage was found to include bomb detonators, an anti-chemical and biological warfare suit and instructions for joining a holy war.
Twelve FBI agents have been sent to various parts of Germany to assist in the investigation.
Alarming pattern
Alarmingly, some experts believe a similar pattern of cells could be operating across Europe.
Professor Paul Wilkinson, the head of the Centre for the Study of Terrorism at St Andrews University, says that though Islamist groups across the continent have different domestic agendas, they share Osama Bin Laden's wider goals.
"It's quite clear that the Bin Laden network had developed bases in Europe some years ago and has been busy extending their work," he told the BBC.
"And its clear from the arrests that have already taken place that we had rather underestimated the extent to which al-Qaeda and other organisations had already developed a network," he added.
UK arrest
As well as Hamburg, the hijackers are also believed to have spent time in the UK, where investigators believe they have made another significant arrest.
Lotfi Raissi, an Algerian-born pilot was detained in London on the orders of the FBI, which has accused him of training four of the suicide pilots involved in the attacks.
In Spain, police say they have broken up a cell of Algerian extremists with alleged links to Bin Laden, while police in Ireland also arrested three Libyans and an Algerian under the Explosive Substances Act.
Meanwhile, the French wing of the investigation is probing a suspected plot to bomb the US embassy in Paris, centring on a number of suspects with apparent al-Qaeda connections.
They believe a number of suspects may have had links with the 19 US hijackers, but their apparent plot was foiled when police arrested members of the group in four countries.