"Responding to the presentation of the initial findings... spokespersons for the Kremlin and the Russian foreign ministry and defence ministry questioned the professionalism, integrity and independence of the Dutch public prosecution service," the Dutch foreign ministry said.
"The Russian ambassador was informed that unsubstantiated criticism like this is unacceptable," the ministry said in a statement, issued in The Hague.
Moscow on Wednesday described as "biased" and "politically motivated" initial findings by a Dutch-led team of international investigators which concluded that the Malaysia Airlines flight was shot down by a missile transported from Russia.
The Boeing 777 passenger jet was blown out of the sky on July 17, 2014 over war-torn eastern Ukraine killing all 298 on board, the majority Dutch citizens.
Criminal investigators from the Netherlands, Australia, Belgium, Malaysia and Ukraine this week said they had "irrefutable evidence" that a BUK missile slammed into the plane and was fired from a field in a part of eastern Ukraine then controlled by pro-Russian rebels.
But the findings stopped short of directly accusing Moscow of involvement in the tragedy.
Koenders said: "Given the convincing nature of the evidence, Russia should respect the results that have been presented, rather than impugning the investigation and sowing doubt."
He called on Russia to "continue to cooperate fully with the investigation and subsequent prosecution and trial" of those responsible.
The tragedy saw the European Union slap tougher sanctions on Russia, blamed by the West for being behind the rebellion. The punitive measures remain in place as the fighting drags on.
But Russia and the rebels have consistently denied any role in downing the plane, and have instead blamed Ukrainian government forces.
Russian foreign ministry spokeswoman Maria Zakharova said Friday the ministry has reviewed the Dutch ministry's press release "on the demarche" regarding Russia's ambassador.
The Russian foreign ministry "drew attention to the Dutch side's total rejection of any reasoned criticism of the preliminary results of the criminal investigation into the crash," Zakharova said in a statement.
"The preliminary results presented by the Joint Investigation Team were officiously portrayed as the only true results to which there can be no doubts or objections," she said.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)