Although the referendum is non-binding, Denmark has promised to honour the result.
The changes outlined in the plan will take effect on June 21, 2009, exactly 30 years after Greenland was granted semi-autonomy from Copenhagen.
Greenland, which is home to the United State's Thule radar base, will be consulted on foreign and defence policy when the changes take effect, although it will not have the final say.
Opinion polls prior to the referendum had suggested that most of Greenland's 57,000-strong population would vote in favour of the plan for increased autonomy.
The plan between Greenland and Denmark also proposes that the island be given rights over its natural resources, which experts say include large oil and gas reserves and mineral deposits.
The vote comes as Canada, Denmark, Norway, Russia and the United States are all staking claims to territory in the Arctic Ocean.
The Danish-Greenlandic commission proposed that "the revenues from activities related to raw materials be distributed to Greenland", in exchange for a drop in subsidies from Copenhagen.
In 2007, the territory received subsidies of 3.2bn kroner ($540m) from Denmark, about 30 per cent of its gross domestic product.
"Self-rule will bring with it only good things for Greenland," Lars-Emil Johansen, who was prime minister of the island from 1991 to 1997, said.
As part of the proposals between Greenland and Denmark, Greenlanders will be recognised as a distinct people in line with international law, while Greenlandic will be recognised as the official language of the territory.
Most of the parties in the local parliament were in favour of self-rule but an opposition movement had opposed it, saying that Greenland still needs considerable support from Denmark.
"With such a tiny population it is impossible to provide the human contributions needed to turn Greenland into a modern and independent state," Finn Lyng, a member of the local Democrats, said.
With its 2.1-million square km surface, 80 per cent of which is covered by ice, Greenland is the world's largest island.