Dortmund prosecutor Ulrich Maass told The Associated Press on Wednesday that the charges involve the World War II murders of three men in the Netherlands while Boere was a member of a Waffen SS death squad that targeted civilians in reprisal killings for resistance attacks.
AP was first to report last month that Maass had quietly reopened the case by beginning his own investigation.
Though Boere was sentenced to death in absentia by a Dutch court in 1949 - later commuted to life imprisonment - German courts have blocked attempts to extradite him or enforce the verdict here. Maass will now seek a German trial for Boere.
"It's high time that this happened, and I'm very pleased that the German prosecutors have finally moved against Boere," Efraim Zuroff, the Simon Wiesenthal Center's chief Nazi hunter, said in a telephone interview from Jerusalem.
"We're running out of time and every day that goes by without these people being put on trial is another chance they have to elude justice."
Boere is among more than 1,000 Nazi cases around the globe that Zuroff's office says were still open as of a year ago.
The son of a Dutch man and German woman, Boere was 18 when he joined the Waffen SS - the fanatical military organization faithful to Adolf Hitler's ideology - at the end of 1940, only months after his country had fallen to the Nazi blitzkrieg.
After taking part in the invasion of the Soviet Union, he ended up back in the Netherlands as part of a unit known as Silbertanne, or Silver Pine, which was composed mostly of Dutch volunteers given the job of killing their countrymen in reprisal for attacks by the anti-Nazi resistance.
The unit is suspected of 54 killings, and Boere admitted after the war while in an Allied prison camp that he took part in three slayings, according to Dutch court documents.
Boere also described his participation in killings during an interview with a Dutch newspaper last year, but said he was working in an official capacity.
"I didn't feel anything, it was work. Orders were orders, otherwise it would have meant my skin. Later it began to bother me, now I'm sorry," he was quoted as saying by the newspaper Algemeen Dagblad.
Boere detailed the killings, almost gunshot by gunshot, in statements to Dutch police preserved in the court file.
The first was in July 1944 - the killing of a pharmacist named Fritz Hubert Ernst Bicknese.
According to Boere's statement, he and fellow SS man Jacobus Petrus Besteman - wearing civilian clothes - walked into the shop and asked the pharmacist if he was Bicknese. When he answered "yes," Boere pulled a pistol from his right coat pocket and fired two or three bullets into Bicknese's upper body, then Besteman fired two or three shots into the pharmacist as he lay on the floor.
The next victim, in September, followed a similar pattern: Boere and an accomplice named Hendrik Kromhout shot bicycle-shop owner Teun de Groot when he answered the doorbell at his home in the town of Voorschoten.
Boere and Kromhout then went to the apartment of F.W. Kusters, and forced him into their car. They drove him to another town, stopped on the pretense of having a flat tire and shot him dead.
"Kusters fell against the garden door of the Villa Constance and sunk to the ground on the other side of the street from the car..." Boere told investigators. "A strong, maybe 10- to 15-centimeter (4- to 6-inch), spurt of blood shot out of Kusters' neck."
Reflecting on that day some 63 years later in 2007, Boere was quoted by the newspaper Algemeen Dagblad as saying that "it was another time, with different rules."
"When we knew for sure we had the right person, we shot him dead, at the door," he was quoted as saying.
For Teun de Groot's son, who has the same name as his father, Boere's late expression of regret is not enough. He told AP that he planned to take part in the prosecution of Boere, as allowed under German law.
"First we have to see if the court will hear the case, and then will it be really real..." de Groot said Wednesday. "But the mood in Germany is such - I think that they want to have an honorable end to this long, sad affair."
The Netherlands has sought Boere's extradition, but a German court in 1983 refused on grounds that he might have German citizenship, and Germany at the time had no provision to extradite its nationals.
A state court in Aachen ruled last year that Boere could legally serve his Dutch sentence in Germany, but an appeals court in Cologne overturned the ruling, calling the 1949 conviction invalid because Boere was not there to present a defense. He had fled to Germany.
It was after the appeals ruling that Maass quietly reopened the case, effectively beginning from scratch.
The murder charges against Boere were filed Tuesday with the state court in Aachen in western Germany near the border with the Netherlands, Maass said.
It was not immediately clear when the court might decide whether to take up the case, and Boere was not arrested after the charges were filed, Maass' office said.
Boere's attorney, Gordon Christiansen, said his client would remain at his upscale old-age home in Eschweiler, near Aachen, while the process is under way.
Christiansen would not comment on the charges, saying he had not yet seen the official documents.
Boere checked himself into an Aachen hospital Monday for unspecified reasons and could not be reached for comment, the old-age home said.
Christiansen said one of his first actions would be to file a motion with the court to determine whether Boere is fit to stand trial.
"I'm no doctor, I can't say myself," Christiansen told AP. "It also depends on how long it takes for this process to begin; one must see."