The issue of Roma deportations from France dominated an EU summit.
Mr Sarkozy told a news conference that Chancellor Merkel had said to him that she intended to follow France's example in dismantling Roma camps.
Mrs Merkel's spokesman denied she had discussed the issue with Mr Sarkozy.
Fresh from a blazing row with the president of the European Commission, President Sarkozy has managed to fall out with his closest ally in Europe, says the BBC's Oana Lungescu, who was at the summit in Brussels.
Heated exchange
Mr Sarkozy told reporters at the summit that Chancellor Merkel had said she intended to dismantle Roma camps in the coming weeks.
He then said: "We'll see how calm German politics will become then".
But promptly after landing in Berlin, the chancellor's spokesman firmly denied that Mrs Merkel had discussed any so-called Roma camps with the French president during the summit or on the margins, let alone their evacuation.
During the summit, Mr Sarkozy clashed with the European Commission over the matter of Roma deportations.
Since August, France has dismantled about 200 Roma settlements and deported about 1,000 of their inhabitants to Romania and Bulgaria. It has also evicted French nationals from illegal traveller settlements.
Earlier this week the EU Justice Commissioner, Viviane Reding, had appeared to compare France's actions to persecutions in Nazi-occupied France.
"The disgusting and shameful words that were used - World War II, the evocation of the Jews - was something that shocked us deeply," Mr Sarkozy said.
He then went on to have a heated exchange with the EU Commission President, Jose Manuel Barroso.
This is an unprecedented row between Brussels and Paris, our correspondent says. But despite all the sound and fury little has changed in practice, as France will continue dismantling illegal camps, she adds.
Mr Barroso recognised that some excessive comments had been made, but insisted that discrimination against ethnic minorities was unacceptable.
"It is true that in the past few weeks, some things have been said that are out of order," Mr Barroso admitted. "But I think we need to leave that on one side now."
Ms Reding, the EU commissioner from Luxembourg, said on Tuesday: "This is a situation I had thought Europe would not have to witness again after the Second World War."
She also urged the European Commission to take legal action against France over the deportations.
Ms Reding later said she regretted interpretations of her statement.
Although France has deported thousands of Romanian and Bulgarian Roma over the past few years, it began accelerating the process last month, as part of a high-profile crackdown on illegal camps in the country.
On Monday, Euro MPs accused the commission of failing to protect the Roma deported from France.
In all, Mr Sarkozy said around 500 camps were dismantled in August, of which 199 were Roma settlements.
About 5,400 people were evicted from the Roma camps, but the majority of those living in the camps were French nationals, the president said.
The president's assertions appeared to contradict a leaked memo from the French interior ministry which surfaced on Monday.
It showed the authorities had been instructed to target Roma camps, rather than deal with migrants on a case-by-case basis, as the French migration minister and the minister for Europe had assured the European Commission.
BBC News
