A police spokesman said there was reason to believe that the suspects - held in a series of police raids in Berlin's Neukoelln district - are among people captured on CCTV footage of the theft.
On March 27, three people walked along the train tracks near Berlin's Hackescher Markt station, propped a ladder against the wall of the Bode Museum and climbed into the building.
They stole the 100-kilogram gold coin known as the "Big Maple Leaf," a commemorative coin issued by the Royal Canadian Mint in 2007, and made off with it using a wheelbarrow they found inside the building.
Special police stand in front of a building in Berlin on Wednesday during raids.
The coin has a face value of Canadian $1mn (US$745,000), although the market price of 100 kilograms of gold is more than $4mn.
One of only five in the world, the coin has a diameter of 53 centimetres and is 3 centimetres thick. It has been part of the Bode Museum's valuable coin collection since 2010.
It features a portrait of Queen Elizabeth II on the front and three maple leaves on the back.
There was no immediate information on Wednesday on the location of the coin.
Earlier this week, police released CCTV footage of the suspects, and announced that tips leading to their capture would be rewarded with up to €5,000 ($5,700).