The court found the parent company is not liable for environmental harm in the Niger Delta, Leadership Newspapers in Nigeria reported.
The lawsuit was filed in October by four Nigerian fishermen and farmers and the environmental group Friends of the Earth, Netherlands.
The order for compensation against Shell Nigeria was the first of its kind in a Dutch court. The dollar amount of damages to be paid was not reported.
The claims by the other plaintiffs were dismissed with the court agreeing with Shell Nigeria that damage was caused by sabotage and by Nigerians tapping pipelines for free oil.
The plaintiffs had contended Shell has failed to maintain its pipelines and has been responsible for spills in the Niger Delta. Shell said cleanup after the spills was done to the standards set by the country's government.