The meat was correctly labelled as horse but was unfit for human consumption as some of it came from animals used by scientists to help produce anti-rabies and other serums.
Police in December made a score of arrests in southern France following a tip-off that 200 horses, including 60 owned by pharmaceutical giant Sanofi, had ended up in abattoirs after their veterinary certificates had been falsified.
Around 11 tonnes of horsemeat that could contain the suspect meat were delivered to five Dutch companies between January and October 2013, the NVWA food safety authority said in a statement.
"Of the 11,000 kilos, we have found around 1,000 kilos," NVWA spokesperson Brenno Bruggink told AFP.
"It's almost 100 percent certain the rest has been eaten."
Dutch junior public health minister Sharon Dijksma said in a letter to parliament that the risk to public health was "very limited or non-existant" because the animals were slaughtered in EU-approved abattoirs.
The case follows a Europe-wide health scare last year when horsemeat was found in millions of ready meals labelled as containing only beef.
Eating horsemeat is regarded as taboo in some European countries, notably Britain, but is still widespread in Belgium, France, Spain and Italy, although consumption is in decline.
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