The BBC says the lost episodes were tracked down by tracing records of overseas shipments of BBC tapes for transmission.
The recovered episodes date from 1967 and 1968 and feature Patrick Troughton, the second of a dozen actors to play the show's time-traveling hero.
They include the six-part series The Enemy of the World and the classic 'robot yeti' story The Web of Fear.
Mark Gatiss, an actor and writer for the modern Doctor Who, told the BBC the find was "thrilling".
It is thought to be the largest haul of missing Dr Who episodes to be uncovered in three decades.
"Every single avenue seemed to have been exhausted, every now and then something turns up - but to have two virtually complete stories out of the blue is absolutely incredible."
New Zealand viewers will be able to see the episodes when they are released on DVD.
The Enemy of the World will be released on 27 November and The Web of Fear will be released early next year.
- AP