© EPAHMS Clyde was refused permission to stop in Rio de Janeiro
Despite continuing tensions with Argentina over the Falkland Islands, the Navy had until now enjoyed cordial relations with its Brazilian equivalent.
But last week, within days of the former left-wing guerilla Dilma Rousseff succeeding Luiz Inacio Lula da Silva as Brazil's president, HMS Clyde was refused permission to stop in Rio.
Miss Rousseff is due to visit Argentina at the end of this month, in her first international trip, with closer trade relations between South American countries due to be discussed.
The decision to block the Royal Navy ship from docking "satisfied" the government of Cristina Fernandez de Kirchner in Buenos Aires, according to the Argentine newspaper Clarin.
HMS Clyde was forced to re-route and instead dock later in Chile, where the Royal Navy still enjoys good relations.
It is the first time that Brazil has refused permission for a British ship to dock in such circumstances and the decision appears to be a clear indication that Miss Rousseff wanted to send a message to Britain and Argentina over the Falklands.
Mark Jones, of the department of political science at Rice University in Texas, said the decision by Brazil suggested that relations with Britain could suffer as Miss Rousseff "plays the anti-colonial card" to satisfy left-wing factions of her Workers' Party.
Miss Rousseff is viewed as a leader who will have to offer greater concessions to the grass routes of her party than her predecessor Mr Lula, who enjoyed popularity ratings of more than 80 per cent.
In the past, Uruguay, Argentina's much smaller neighbour, has twice stopped British ships mooring in Montevideo to show solidarity with Buenos Aires.
On the last occasion HMS Gloucester, a type 42 destroyer, was banned from entering Montevideo in September 2010 for supplies and fuel despite having been authorised to do so days before.
President Kirchner has tried a number of tactics to make it more difficult for the Royal Navy to operate in the waters around the Falklands.
One decree demands that all ships travelling to or from the Falklands through Argentine waters must request prior permission from the country's coastguard.
Argentina has repeatedly attacked Britain's refusal to discuss the sovereignty of the islands with Jorge Arguello, its ambassador to the UN, recently questioning whether Britain deserved its seat on the UN Security Council.
HMS Clyde is an offshore patrol vessel that is permanently deployed to the South Atlantic with a change of crew every six months.
In May last year it was involved in the rescue of a British family whose yacht was in danger of sinking 1,000 miles east of the Falklands.
A spokesman for the Foreign Office said: "We can confirm that HMS Clyde had planned to make a routine port stop in Rio de Janeiro in early January.
"Brazil did not grant diplomatic clearance this time. We respect Brazil's right to make such a decision. We have a close relationship with Brazil.
"The UK-Brazil defence cooperation treaty signed last September is a good example of our current strong links."
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