Yameen also declared a state of Emergency in Maldives on Monday.
Legal Affairs Minister Azima Shakoor read out the emergency decree on state television, giving security forces sweeping powers to make arrests, and curtailing the powers of the judiciary.
Armed police have broken down the door of another former president Maumoon Abdul Gayoom.
The government did not immediately comment on soldiers going inside the building.
"This declaration is unconstitutional and illegal", former president Mohamed Nasheed, the country's first democratically elected leader, said in a statement. "The Supreme Court verdict, in a way, means transfer of power", said a leader from MDP, which is led by Nasheed.
'Certain rights will be restricted (but) general movements, services and businesses will not be affected, ' the president's office had said in a statement about the emergency.
Security forces "blockaded and locked the Supreme Court building from outside and hence the justices are without any food", Maldives' former Attorney General Husnu Al Suood tweeted.
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But the government, which has ordered police and troops to resist any attempt to arrest or impeach Yameen, said the court was not above the law.
Maldives' Supreme Court late on Thursday ordered immediate release of all nine political prisoners.
Heavily armed troops and police special operations units stormed the Supreme Court in the early hours, the court said on Twitter, as police used pepper spray to disperse hundreds of people gathered outside. "But respect for human rights must not become another casualty of this ongoing political crisis", Dinushika Dissanayake, Amnesty International's deputy South Asia director, said in a statement. This could lead to the opposition evicting the Speaker and passing no-confidence motions against government officials. But Modi called off a visit to Maldives in 2015 during a tour of Sri Lanka, Seychelles and Mauritius following reports of a crackdown by Yameen on the opposition. When those lawmakers return, Yameen's Progressive Party of the Maldives will lose its majority in the 85-member parliament, which can result in the legislative body functioning as a rival power to the president. As the situation appears to be spiralling out of control, India, along with the United States, European Union and the United Nations, made an appeal to the Yameen government to respect the court ruling and restore democratic practices.
He was granted medical leave in 2016 and traveled to Britain where he was granted asylum.
In addition to ordering the release of the political prisoners, the court also reinstated 12 politicians who had been ousted for switching allegiance to the opposition.
But the country lost much of its democratic gains after Mr Yameen, who has maintained a tight grip on power, was elected in 2013.
He had been set to run for re-election this year virtually unopposed, with all of his opponents either jailed or exiled, until the current crisis. The move prompted Nasheed, now in self-exile, to say he would return to contest elections that are expected to be held later this year. He lost the 2013 election to Yameen, then was convicted under Maldives' anti-terrorism laws in a trial widely criticized by global rights groups.