Quoting Arūnas Bubnys in The Vanished World of Lithuanian Jews, page 209:

In August 1941 Kaunas Jews were murdered in Kaunas Fourth Fort and from October 1941 in the Ninth Fort. Here executions were carried out until the very end of [Axis] occupation. The largest mass murder of Kaunas Jews took place on 29 October 1941. The evening before the murders the Gestapo selected Jews from the Kaunas ghetto. Around 10,000 people were selected for death. They selected families with many children, physically weak persons, old people and the sick for murder.

Members of the TDA, later called the First Police battalion, also took part in the selection of ghetto prisoners. On 29 October the condemned Jews were driven out of the ghetto to the Ninth Fort where they were shot in huge previously‐dug pits. According to Jaeger’s report 9,200 Jews were killed in the fort on 29 October of whom 2,007 were men, 2,920 were women and 4,273 were children. Jaeger referred to these murders cynically as “the cleansing of the ghetto from unnecessary Jews.”¹⁰

Yitzhak Arad’s The “Final Solution” in Lithuania in the Light of German Documentation:

Lithuania was the first country in occupied Europe in which mass extermination of Jews took place. During the first four and a half months of [Axis] occupation — from the end of June to the beginning of November 1941 — more than 80% of Lithuanian Jewry was killed.

This “achievement” was made possible by the fact that the Einsatzgruppen, S.D. and Security Police units, who carried out the mass murder and who all together numbered only several hundred men, were assisted by thousands of volunteers from among the local populace.

Thus, for example, Brigadeführer Stahlecker, the commander of Einsatzgruppe A, wrote in this report of October 15, 1941: “The active anti‐Semitism which flared up quickly after the German occupation did not falter. Lithuanians are voluntarily and untiringly at our disposal for all measures against Jews; sometimes they even execute such measures on their own.”¹⁹

[…]

Peschel, chief of the Labor Office, wrote to von Renteln in September or the beginning of October, urging him to allow the surviving Jews to continue working, and he approached the Wehrmacht authorities in Kovno with the same request. Gebietskommissar Cramer, favored leaving the Jewish artisans alive.

Thus, Herrman reported on a meeting (which was attended by von Renteln, Jäger, Cramer, Peschel, the Lithuanian First Councillor General in Lithuania, Petras Kubiliūnas and others) that took place in Kovno, at which it was decided to write to Riga and urge that the Jewish artisans and their families be left alive. Peshel went to Riga to intervene personally on behalf of those Jews who dwelt in the ghettos of Vilna, Kovno and Shavli.

An affirmative reply was received in Kovno on October 20 or 21. The Security Police and S.D. agreed to spare the artisans, but they insisted on the liquidation of intellectuals and members of the liberal professions as well as of those physically unfit for work.²⁶

Karen Sutton’s The Massacre of the Jews of Lithuania:

In Kaunas, the mass shootings continued unabated in August–October 1941. German records recount the use of auxiliary Lithuanian personnel much as in Vilnius. The “small ghetto” was liquidated in early October. According to Jäger’s summation, 315 Jewish men, 712 women and 818 children were shot on October 4.

On October 28, during the Grosse Aktion, approximately 9,200 were shot at Fort IX. This marked the last mass shooting of Jews from the Kaunas ghetto for over a year. During that time, instead of “cleansing local elements,” the execution squad of Einsatzkommando 3 exterminated thousands of Jews who had been transported from the Reich for “resettlement in the east.” A resident of the Kaunas ghetto recorded:

The next morning when I got up I went to the kitchen window, which faced the highway leading to the Ninth Fort and — God Almighty, there were columns of one hundred each slowly moving up the road […]. These were Austrian Jews being taken to the East for work. The Ninth Fort had suddenly become an execution ground for European Jewry. The local anti‐Semitic collaborators in the European countries helped the Nazis round up the Jews. The Germans then transported them to Lithuania and our local collaborators, our peaceful neighbors of years past, did the final shooting […]. God Almighty, was there ever a Jesus Christ who walked this earth of ours? Was this what He taught them?²⁰

(Emphasis added in all cases. I know that the text here says October 28, but it seems that the massacre probably continued into the early morning of October 29.)

Joachim Tauber in Complicated Complicity: European Collaboration with Nazi Germany During World War II, page 131:

In the district of Kaunas, Jewish properties were rented to “Aryan” inhabitants, with the contracts of the previous Jewish owners being openly noted in the records.⁴²