The Police Department said early on Friday that a report about the desecration of the monuments in Agrastai Street had been received at around 6 p.m. on Thursday, adding that a pre-trial investigation had been opened into the violation of public order.
Julija Samorokovskaja, spokeswoman for Vilnius County Police, told BNS later on Friday that the stones had been defaced with the "Z" and "V" symbols.
Simonyte denounced the desecration of the Paneriai memorial to Holocaust victims as a "clear provocation".
"This is a clear provocation aimed at antagonizing the public in Lithuania," the prime minister said in a statement on Friday.
"In one of the most tragic places in Lithuania's history, where the Nazis and other criminals murdered thousands of innocent people, the provocateurs have splashed yet another symbol of hatred," she said.
Paneriai is the largest site of mass killings organized and carried out by the Nazis in Lithuania. Some 50,000 to 70,000 people, mostly Jews from and around Vilnius, were killed there between 1941 and 1944.
The Z symbol has emerged recently after Russia started its invasion of Ukraine.
The Russian Defense Ministry explained in early March that the letter "Z" on military equipment stands for "Za pobedu" ("For victory"), while the "V" symbol stands for "Sila v Pravde" ("Strength is in the truth") and "Zadacha budet vypolnena" ("The task will be completed").