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Mr Blair, 55, was last seen on March 8 when he launched his nine-metre aluminium boat Erie in the Marlborough Sounds.
His boat was discovered around 200km off the coast of Taranaki by a Royal New Zealand Air Force Orion on Friday evening.
Attempts to secure it and bring it to shore have been hindered by stormy weather and heavy seas, but authorities managed to board the vessel overnight.
Mr Blair was not on board, and police said there was no immediate indication on what happened to him.
Police officers onboard the Navy vessel HMNZS Wellington battled 10-metre swells to board the Erie.
The naval vessel will now attempt to tow Mr Blair's boat to New Plymouth.
Because of rough sea, it was not expected to arrive today, police said.
"Once the Erie is back in port a detailed examination will be made to try and find some indication as to what has happened to Mr Blair," police said.