The Passport Office chief executive Paul Pugh said the agency was facing a challenging situation the like of which has not been seen in recent years, after apologising for the delays.
He said the Passport Office is dealing with 480,000 applications. Around 90% are being processed within targeted time.
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The Philippine president famously called the Pope a "son of a bitch" and told Barack Obama to "go to hell".
Those still left after the demolishing of the 'Jungle' camp were seen wrapped in blankets as they prepared to sleep rough.