But UK officials said the accusations of militarisation were "absurd".
UN chief Ban Ki-moon earlier called on both sides to avoid an "escalation" in tensions over the Falkland Islands.
The two countries went to war in 1982 over the British overseas territory.
Mr Timerman told a news conference at the UN in New York that the UK was "militarising the region", repeating accusations made by Argentine President Cristina Fernandez de Kirchner earlier this week.
"Argentina has information that, within the framework of the recent British deployment in the Falklands, they sent a nuclear submarine with the capacity to transport nuclear weapons to the South Atlantic," Mr Timerman said.
He did not elaborate on the information, but said the vessel was Vanguard-class, a group that carries Trident nuclear missiles.
AnalysisArgentina's foreign minister came armed with maps and photographs to make his case to the Secretary General, the head of the Security Council, and the press.
Britain, he claimed, is bringing new state-of-the art weapons into the South Atlantic, and has sent a nuclear submarine into a nuclear-free weapons zone. It is a threat to regional security he said.
The British ambassador Mark Lyall Grant called the accusations an escalation. He would not be drawn on the location of Britain's nuclear submarines, but said they stayed in international waters. He also spelled out in detail Britain's stance that the dispute over the Falklands is not one of sovereignty, as Argentina insists, but one of self-determination: the islanders must be allowed to determine their own fate, he said, and they want to be British.
In response, Britain's UN envoy Mark Lyall Grant said the government does not comment on the "disposition of nuclear weapons, submarines etc".
And he dismissed the accusation that the UK was militarising the situation as "manifestly absurd".
"Before 1982 there was a minimal defence presence in the Falkland Islands," he said.
"It is only because Argentina illegally invaded the Falkland Islands in 1982 that we had to increase our defence posture. Nothing has changed in that defence posture in recent months or recent years."
The UK had earlier said it was carrying out routine operations in the South Atlantic.
The BBC's Barbara Plett at the UN in New York says the dispute is raised every year at the UN, and usually involves both sides sending letters to the secretary general.
But this year is the first time Argentina has provided such a detailed and public account of its grievances, she says.
It is not clear if Argentina plans to pursue any further action at the UN beyond the current protest.
The UN General Assembly has already passed non-binding resolutions urging the two to solve the dispute through negotiations.
The status of the islands, known in Argentina as the Malvinas, is still a highly sensitive issue for Buenos Aires.
In recent months, the Argentine government has stepped up its rhetoric on the issue and has sought support among its South American neighbours.
In December, regional trading bloc Mercosur closed its ports to ships flying the Falkland Islands flag.