The men and boys were among 5,000 Bosniaks sheltering with Dutch United Nations peacekeepers in Bosnia-Hercegovina at the time.
The Srebrenica massacre is considered Europe’s worst since the Second World War.
However, the Dutch state was cleared over the deaths of more than 7,000 other men killed in and around the area Srebrenica.
A district court in The Hague said Dutch peacekeepers in Srebrenica, a Bosnian Muslim enclave in Bosnian Serb-held territory, could have known the 300 men who had sought refuge in their base in the village of Potocari would be murdered if deported from the Dutch compound.
“By co-operating in the deportation of these men, Dutchbat (the Dutch battalion of the UN forces) acted unlawfully,” said judge Larissa Alwin.
But the court said the Netherlands was not liable for the deaths of those who had fled into the forests surrounding Srebrenica, where many were later buried in mass graves.
A lawyer for the relatives, Marco Gerritsen, said he would study the 89-page ruling before deciding whether to appeal this decision.
The ruling could set a precedent with implications for future peacekeeping deployments by the Netherlands or other countries.
During the Bosnian war, the Dutchbat had been deployed to protect Srebrenica, which had been designated a safe haven by the UN, but surrendered to the much larger Bosnian Serb army.
“At the moment that the men were sent away, Dutchbat knew or should have known that the genocide was taking place and therefore there was a serious risk that those men would be killed,” said judge Peter Blok.
The three-year Bosnian war, in which at least 100,000 people were killed, was the bloodiest of a series of conflicts that accompanied the break-up of Yugoslavia in the 1990s.
The case was brought by the Mothers of Srebrenica, a group representing surviving relatives of the victims.
They had failed in their bid to have a court find the UN responsible for the massacre.
“The court has no sense of justice,” said Munira Subasic, a representative of the’ group.
This, she said, means many of the relatives of the victims will not be entitled to compensation.
She added: “How is it possible to divide victims and tell one mother that the Dutch state is responsible for the death of her son on one side of the wire and not for the son on the other side?”
Two key figures of the wartime Bosnian Serb leadership – one-time president Radovan Karadzic and General Ratko Mladic – are on trial at The Hague.