The three German nationals who were arrested are suspected of "serious gang robbery and two counts of arson".
In March, prosecutors and police said they had determined that an Audi S6 used in the theft and later set alight in a Dresden garage was sold to an unidentified buyer in August.
However, Dresden police spokesman Thomas Geithner admitted, "We'd have to have a lot of luck in order to find them a year after the crime".
Germany's Bild newspaper reported that the stolen jewels were worth up to $1.19 billion.
One of its best-known treasures - the 41-carat Dresden Green Diamond - was away on loan to New York's Metropolitan Museum of Art at the time of the break-in. They will be presented to an investigating judge in Dresden on Tuesday.
The three arrested men have not been named, but they are understood to be members of the Remmo Clan, one of Berlin's most powerful organised crime groups.
Police issued photos of two others, wanted on the same charges, identifying them as Abdul Majed Remmo, 21, and Mohamed Remmo, 21.
The searches, focused on Berlin's Neukoelln district, did not immediately turn up any of the missing treasures.
"Nobody should believe that he set himself above the rules of the state", Geisel said.
POlice have offered 100,000 euros in reward for information leading to the arrest and/or conviction of the suspects.
Security camera footage showed two men breaking into the museum through a grilled window in the early hours of November 25.
Police had responded within five later - but the crooks had already fled.
The stolen objects included a sword featuring a hilt encrusted with nine large and 770 smaller diamonds and a shoulder piece that contained the famous 49-carat Dresden white diamond.
Among the haul, the thieves stole items of jewelry that belonged to the 18th century Saxon ruler Augustus the Strong.
The sprawling treasure collection survived the bombing of Dresden in the Second World War, only to be seized as war booty by the Soviet Union. It was returned to the museum in 1958.