Officials confirmed both countries had bowed out of meetings, with one source saying it was not acceptable for the United States to take charge of the overhaul process as it is leaving the WHO. President Trump has been fiercely critical of the United Nations agency over its handling of the coronavirus pandemic and in July announced the US would be pulling out of the WHO.
America will officially withdraw from the body next year.
Mr Trump had claimed the WHO had leaned too close to China, where the novel coronavirus was first detected late last year.
The WHO has dismissed his accusations.
While European leaders have also been critical of the Organisation’s handling of the crisis, they have not gone as far as to withdraw their membership.
The departure of Paris and Berlin from the negotiating tables is a major setback for Mr Trump just three months before Americans head to the polls for the November 3 election.
The Republican president had hoped to issue a common roadmap for a sweeping overhaul of the WHO in September.
A senior European official involved in the talks said the US should not lead the meetings if it did not want to remain a member.
They said: “Nobody wants to be dragged into a reform process and getting an outline for it from a country which itself just left the WHO.”
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The ministry said: “The US should not take the lead in the WHO reform process after announcing their intention to leave the organisation.”
Asked about the position of France and Germany, a senior Trump administration official said the decision of both countries to quit was regrettable.
The official said: “All members of the G7 explicitly supported the substance of the WHO reform ideas.
“Notwithstanding, it is regrettable that Germany and France ultimately chose not to join the group in endorsing the roadmap.”
The talks on WHO reform began about four months ago.
There have been nearly 20 teleconferences between health ministers from the Group of Seven industrialised nations, and dozens of meetings of diplomats and other officials.
A deal by the G7, which also includes Japan and Canada, would facilitate talks at the G20 and United Nations.
Any changes would have to be agreed with China, Russia and other major governments not in the G7, at a UN meeting.
It is unclear whether a G7 summit in the US, at which President Trump hopes leaders will endorse the roadmap, will now go ahead in September as planned.