The former fruit and vegetable warehouse -- now with a capacity for 2,000 corpses -- was temporarily comandeered as part of the government's emergency Plan Blanc, or "White Plan."
The government enacted the nationwide disaster scheme to cope with a health crisis caused by a two-week heatwave the health ministry said had resulted in between 1,500 and 3,000 deaths, most of them frail and elderly people.
The morgue was opened after funeral homes in the Paris region became full up.
The morgue which was opened Friday took on 35 victims overnight.
The Plan Blanc is providing extra hospital beds and staff, and authorises the setting-up of temporary morgues to cope with the deaths caused by stifling temperatures, which had hovered around 40 degrees Celsius (104 degrees Fahrenheit) until dropping late Wednesday.
Originally conceived to respond to terrorist attacks, natural catastrophes or epidemics, the measure was initially implemented Wednesday in the Paris region and later extended to the entire country.
The morgue will likely not fill to capacity, according to Martial Mazar, director of the funeral undertaker service for the Seine-Saint-Denis departement north of Paris and also responsible for the makeshift Rungis morgue.
He said the refrigerated morgue will likely take on "no more than 700 corpses until Monday or Tuesday," citing a fall in temperature and the fact that hospitals and funeral homes will likely free up space.
The morgue will remain in operation for two weeks, "time for families to organize funerals," Mazar added.
The government has been taken to task for its tardy response to the heatwave, with the Liberation daily calling the situation a "massacre" and accusing the government of having done "too little, too late."
Earlier, Health Minister Jean-Francois Mattei, in an interview on France Inter radio, called the situation "a true epidemic, with everything that means in terms of the number of victims" and compared it to a 1995 heatwave in the US city of Chicago that had claimed 700 lives.
The row turned nasty Friday, with one deputy accusing families of abandoning their elderly relatives while the government blamed a Socialist labour law for leaving hospitals understaffed.
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