"It's not my time to die," exhausted Police Minister Serge Gelle said as he recovered on a stretcher.
A security official travelling with him in the helicopter also survived the crash.
The team had been flying to inspect the site of a shipwreck in the north-east of the Madagascar on Monday night.
The number of people confirmed dead in that accident has risen to 85 after 21 more bodies were retrieved on Wednesday, the maritime agency said, the AFP news agency reports.
About 50 people have so far been rescued, with three others still missing, it added.
The vessel was a cargo ship that was not authorised to carry passengers, and was overloaded and water flooded its engine, an agency official was quoted by Reuters news as saying.
On Twitter President Andry Rajoelina mourned those who died and also paid tribute to Mr Gelle and the other officer, who arrived in the seaside town of Mahambo separately.
The helicopter's pilot and another military officer on board are still missing, he said.
Speaking on Tueday, Mr Gelle, 57, said his helicopter came down after it caught a gust of wind, and he swam from "7:30 last night , until 7:30 this morning," to Mahambo.
He said he had no injuries but added that he was feeling cold.
"I would just like you to broadcast this video for my family to see, my colleagues to see, the government members to see. [I am] alive and well," Mr Gelle told locals at Mahambo.
Police chief Zafisambatra Ravoavy told AFP that Mr Gelle had used one of the helicopter's seats as a flotation device.
"He has always had great stamina in sport, and he's kept up this rhythm as minister, just like a 30-year-old... he has nerves of steel," Mr Ravoavy said.
Mr Gelle had served in the police for three decades before his appointment as minister in August.
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