Punithan Genasan, a Malaysian aged 37, was given the sentence after being convicted of masterminding a drug trafficking operation.
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He took part in the virtual hearing from prison while his lawyer and the prosecutors joined in the call from other locations.
Human Rights Watch said the death penalty was already cruel and inhumane, and the use of Zoom to announce it made it worse.
"It's shocking the prosecutors and the court are so callous that they fail to see that a man facing capital punishment should have the right to be present in court to confront his accusers," the group's deputy Asia director, Phil Robertson, said Wednesday.
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"Singapore tries to hide from the world that it executes scores of people every year but by remotely sentencing a man to die in this case, they have brought back welcome attention to their inherently rights-violating practices," he added.
It is believed to be the first time the death sentence has been delivered remotely in Singapore.
Genasan's lawyer said he had no complaints with the way the hearing was conducted, but said he would meet with his lawyer on Friday to discuss an appeal.