Le Monde's reports "contain inaccurate and misleading information" about the US's Prism programme, Clapper said in a statement Tuesday and he specified that the "allegation that the National Security Agency (NSA) collected more than 70 million 'recordings of French citizens' telephone data' is false".
It also noted that Clapper did not deny its report that the US had spied on French embassies end diplomatic missions, including the French representation at the UN.
The US Director of National Intelligence conceded that the US "collects intelligence to protect the nation, its interests and its allies from, among other things, threats such as terrorism and the proliferation of weapons of mass destruction".
French leaders have dubbed the snooping "unacceptable" but now admit there is little more they can do.
President François Hollande's spokesperson Najat Vallaud-Belkacem said Wednesday that Paris and Washington had agreed to work on new "bilateral cooperation between the French and American intelligence agencies" in the wake of the scandal.
US Secretary of State John Kerry went on to Italy on Tuesday night after meeting French Foreign Affairs Minister Laurent Fabius in the morning.
He was to meet Italian Prime Minister Enrico Letta, who was expected to ask for an explanation on reports that the NSA spied on Italian international communications.
Mexican President Enrique Pena Neta has ordered an "exhaustive probe" into claims that the NSA hacked his emails while he was campaigning to be elected and those of his predecessor Felipe Calderon while he was in office.
Brazilian President Dilma Rousseff has called off a planned visit to the US in protest at the interception of communications from and to her office, as well as in embassies and the offices of national oil company Petrobras.