Spiegel magazine had reported that Health Minister Jens Spahn of Merkel's CDU party had spent a billion euros on masks that allegedly turned out to be below par.
In a bid to use them up, his ministry looked at distributing them to the disadvantaged, according to the report.
But after the SPD-led labour ministry opposed the move, the masks finally ended up in the national reserve as emergency stocks in case of a new crisis.
The report sparked an outcry, prompting the leaders of junior coalition partner SPD to demand Spahn's resignation.
"Jens Spahn's behaviour is inhumane," charged SPD co-leader Saskia Esken.
As accusations flew, Merkel rode to Spahn's rescue.
At a meeting of the CDU top brass on Monday, she said the accusations were "simply not backed up by facts", party sources told AFP.
"It's about putting the fight against the pandemic in a bad light," she said, according to party sources. "One must calmly and clearly tell the SPD that that has nothing to do with the facts."
The decision for the masks to make up the national reserves was "made with the SPD," she said, adding that "we all support Jens Spahn".
CDU party chief Armin Laschet, who is her conservative would-be successor, also accused the SPD of "seeking to get points through a negative campaign attempt".
The health ministry sought to set the record straight, saying that the masks in question met "infections protection standards" and had been tested including by medical experts.
The disagreement with the labour ministry had been over which set of certification criteria to apply, it added.
Merkel's CDU has been in an awkward partnership with the Social Democrats since 2013, something which the general election on September 26th is expected to end.
The centre-left SPD has seen a big drop in voter share over the years, and has repeatedly accused Merkel's conservatives of getting the credit for policies they spearheaded.
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