The raids took place and a car was seized in the district of Neukolln, German news agency DPA reports.
The suspected robbers are believed to have used a ladder to get into the museum and a wheelbarrow to carry the 21in-coin away in March.
Last week, police released CCTV footage of suspects at a local train station.
The Canadian “Big Maple Leaf” is made of 220lb of pure 24-carat gold – which means it is worth about $4.2 million, despite a lower nominal face value.
The giant coin has not been found and investigators say they believe it may have been melted down and sold.
They are said to be at a loss as to how the thieves broke bullet-proof glass inside the building and evaded burglar alarms.
As well as making the arrests on July 12, police seized a car where a balaclava and knife were found.
Sources inside the investigation say the suspects come from a “large Arab family” with alleged links to organized crime.
The Big Maple Leaf coin was minted by the Royal Canadian Mint in 2007, and certified by Guinness World Records as the world’s largest gold coin. Five coins were made at the time.
The giant coin is 3cm (1.18in) thick, 53cm in diameter, and with likeness of Queen Elizabeth II on one side, as Canada’s head of state. The other side shows the Canadian national symbol, the maple leaf.
Canadian Mint says: “Why did the Royal Canadian Mint make the world’s purest and largest gold bullion coin? Because we can.”
The giant coin was held in a coin cabinet at the Bode Museum as one of more than 540,000 objects, but German media report only the “Big Maple Leaf” was stolen.
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