Mahmoud Mohammad Issa Mohammad was transported by charter flight to Lebanon, said Immigration Minister Jason Kenney, who described the protracted case as "almost a comedy of errors."
"After a 26-year stay in Canada, we finally succeeded in deporting this convicted, terrorist killer," Kenney told an Ottawa news conference.
Border agents escorted Mohammad on the charter flight, which also carried a medical team as a precaution because of his undisclosed health issues.
The case had become a symbol of a broken immigration system, said Kenney.
Mohammad was convicted as a terrorist two years after making headlines in 1968, when he and an accomplice attacked an Israeli commercial airliner at the Athens airport. One of the plane's passengers was killed.
A Greek court convicted Mohammad of manslaughter and other charges, sentencing him to 17 years in jail.
But he was freed a few months later as part of a deal to end a hostage-taking aboard a plane hijacked by another Palestinian terrorist group.
After moving from place to place and then obtaining residency in Lebanon, Mohammad eventually made his way to Canada in 1987 and entered the country under a false name.
In his application for residency, Mohammad denied being convicted of any crime.
He also claimed he had no involvement as an adult with any political organization, although he had been a member of the Popular Front for the Liberation of Palestine.
The following year, Immigration Canada caught him and ordered him deported.
He re-styled himself as a Palestinian freedom fighter and launched one appeal after another, while living with his family in a modest home in Brantford, Ont.
Those appeals finally came to a halt under new laws introduced by the Conservatives.
"This case is almost a comedy of errors, with delays, with a system that was so bogged down in redundant process and endless appeals that it seemed to some that we would never be able to enforce the integrity of Canada's immigration system," said Kenney.
Mohammad is now a grandfather. His two adult daughters and son have put down roots in Canada.
And although he lived peacefully in southern Ontario for the last two decades, Kenney said the man's 40-year-old criminal record and the circumstances through which he entered Canada, compelled the government to expel him.
Kenney said he hopes that the Faster Removal of Foreign Criminals Act, the use of biometrics and reforms to the asylum system will help ensure that no other convicted terrorist can remain in Canada for such an extended period.
The Centre for Israel and Jewish Affairs applauded the deportation, calling it a relief.
"Although long delayed, justice was ultimately not denied in this case, said the centre's CEO, Shimon Fogel.
"Just as it is critical that we provide swift and compassionate support to legitimate refugees, it is likewise essential that we prevent Canada from being used as a safe haven for terrorists," he said.
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