The Arnhem-Leeuwarden court told prosecutors "to conduct a closer investigation into the destruction or damage to buildings which could have posed a life-threatening danger to others" between January 1, 1993 and April 14, 2015 in the northern Groningen province.
The Dutch NAM company, which is half-owned by Shell and ExxonMobil, has been extracting gas from the massive Groningen gas field since 1963.
But the area has been plagued by a series of minor earthquakes which grew in number as gas extraction increased, causing major damage to homes, farm homesteads and historic buildings.
This prompted a second complaint, with the court finding today that a full investigation into whether there had been any criminal liability "has been neglected".
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"A proper investigation must now first be conducted, after which a decision about whether to prosecute will be made," the court added in a statement.
NAM, in a separate statement, said it was "surprised by the verdict."
"But it doesn't necessarily mean that the NAM will be sued. It depends on the outcome of the investigation," it said.
Production has been steadily cut back over the past two years from about 42.5 billion cubic metres in 2015.
After Norway, The Netherlands is western Europe's second-largest gas producer and although falling, natural gas exports last year constituted 2.0 per cent of the country's total revenue.
But a number of tremors over recent years resulting from the collapse of empty underground pockets have frightened residents and caused major damage.