Officials said on Saturday that Rayed Mohammed Abdullah Ali, a United States-qualified pilot, was deported late last month after immigration officials raided his home in Palmerston North, where he had joined the local aero club.
David Cunliffe, the immigration minister, said in a statement that Ali was considered a threat to national security because of his activities in New Zealand and because he was "directly associated with" those responsible for the 2001 attacks on the US.
He was sent back to Saudi Arabia under escort.
Cunliffe would not comment on what specific information the government had on Ali, or where it came from, but told the Weekend Herald newspaper: "We're satisfied he is the right man."
He referred to the US government's September 11 Commission Report regarding "Rayed Abdullah" who lived and trained in Phoenix with Hani Hanjour, the Saudi believed to have piloted Flight 77 into the Pentagon.
Ali had arrived in New Zealand in February on a student visa saying he wanted to be a commercial airline pilot and needed to build up his flying hours and achieve an English language qualification.
Cunliffe said Ali's true identity became apparent only after he arrived in New Zealand and "he used a variation of his name in applying for entry".
Ali was only the second person deported under a section of New Zealand's Immigration Act, which has no right of appeal.
Canada frees suspect
In Canada, the Federal Court on Friday dismissed the government's appeal to overturn a previous decision to free from prison Algerian national Mohamed Harkat, whom it suspects of belonging to Al-Qaeda.
On May 23, another federal court had granted Harkat a conditional release as he awaited a ruling on an extradition request from Algeria.
However, he was required to wear an electronic bracelet, pay a $31,500 bond and stay within the confines of his home in Ottawa if released.
Canada's public safety minister appealed the court's decision, saying Ottawa had "reasonable grounds to believe that Mr Karkat poses a risk to national security" and should not be released.
But Justice Robert Decary refused to overturn the order, saying there was no evidence to show Harkat "represents a threat or a danger".
Harkat was arrested in December 2002 at his Ottawa apartment under a 1991 legal measure authorising the expulsion or imprisonment of a Canadian resident or an immigrant suspected of posing a threat to national security.
The Canadian Security Intelligence Service suspects Harkat of having trained in a terrorist camp in Afghanistan and of belonging to an al-Qaeda sleeper cell.