France's health ministry confirmed the toll on Thursday after being accused by doctors of underestimating the scale of the disaster.
A statement from the ministry said: "the number of deaths directly or indirectly linked to the heat during this period can be estimated at around 3000 for all of France."
Health Minister Jean-Francois Mattei added: "The (death) figures are high, perhaps even very high.... We can now talk about what happened as a true epidemic, with everything that means in terms of the number of victims."
The acknowledgement followed days of warnings from doctors, police and undertakers that bodies had piled up staggeringly quickly in the 40C (104F) temperatures.
"The (death) figures are high, perhaps even very high.... We can now talk about what happened as a true epidemic"
An association of hospital emergency room doctors, AMUHF, said on Thursday it estimated at least 2,000 people had died during the hot weather.
"The figures are becoming catastrophic," the head of the association, Patrick Pelloux, said.
"We can talk about thousands of victims, even though we can't yet fully measure the phenomenon."
A hospital workers' union leader, Francois Freisse, said even though the heatwave has receded heat-stroke victims are still expected in the coming days.
He also singled out the government, saying "the authorities didn't react immediately when faced with the seriousness of the situation."
Pelloux called on the government to expand nationally an emergency medical plan put in place in and around Paris on Wednesday.
The plan provides extra hospital beds and staff, and permits temporary morgues to be set up.
Prime Minister Jean-Pierre Raffarin announced the plan after city officials and unions raised the alarm.
But Raffarin brushed aside a call for him to resign launched by the opposition Green party.
He said: "This is not the time for arguments. I feel that I did all what was necessary at the right time."
However, the pressure is clearly mounting on the government.
The Liberation newspaper used the one-word headline "massacre" on its front page, and lashed the government in an editorial for having done "too little, too late."
It added most ministers have been too reluctant to cut short their summer vacations, and demanded the government give serious thought to global warming, energy production and water management.