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The episode, which ran on Monday night, was the last for the year and concluded with one character dying following the crash.
Earlier yesterday, two bodies were retrieved from a "mangled wreck" after a light aircraft crashed into mudflats at Raglan about 3.20pm.
A spokesperson from TVNZ apologised to any viewers who might have found last night's episode disturbing following the Raglan crash.
"We apologise to any viewers who found this episode upsetting and our condolences are with the victims' family and friends," the spokesperson said.
"This episode was filmed some weeks ago, but unfortunately its broadcast coincided with a real-world tragedy."
Emergency services were called to the crash in Raglan shortly after 3.20pm.
The aircraft crashed onto mudflats in the Kaitoke Harbour, locals nearby likening the sound of the incident to a car crash.
The bodies of the plane's two occupants were retrieved by emergency services just before 6pm last night and the scene was being examined.
The aircraft crashed during low-tide and has since been surrounded by water and would be left in the water overnight.
In last night's episode, Shortland Street character Chris Warner decided to charter a private plane to take him and his colleagues to his family lodge for the holidays.
However, the plane crashed after the pilot suffered a heart attack. The fates of injured father and son Mo and Jack Hannah were left hanging.
Shortland Street will return to TVNZ 2 on January 14.