A small local self-defence unit was created to defend the village against repeated Soviet partisans' raids. The village of about 60 households and 300 inhabitants was not fortified but the villagers were armed with a few rifles.

On January 29, 1944, the village was attacked by Soviet partisan units under the command of the Central Partisan Command in Moscow.

The raid was carried out by 100–120 partisans from various units including 30 Jewish partisans from the 'Avengers' and 'To Victory" units under the command of Jacob (Yaakov) Prenner.

According to the findings of the Institute of National Remembrance (investigation still in progress), at least 38 people were killed and about a dozen injured, although earlier reports stated higher numbers of deaths.

Notified about the assault, the 253rd Lithuanian Schutzmannschaft battalion soon arrived at Koniuchy but did not find any Soviet partisans.

The attack was carried out by the Soviet partisan units 'Death to the Fascists' and 'Margiris' from the Vilnius Brigade of the Lithuanian Partisan Staff and 'Death to the Invaders' of the Kovno Brigade.

Following the attack, a message sent from Genrikas Zimanas (Henoch Ziman), head of the 'South' Partisan Brigade, to Antanas Sniečkus, communist leader and chief of Headquarters of the Lithuanian Partisan Movement, read as follows:

"On January 29, a joint group of Vilnius and Kovno partisans, as well as a special group from General Headquarters burned down the most ardently resistant village of the Eišiškės County, Kaniūkai."

Evaluations and controversy

There are controversies surrounding the significance of the Koniuchy incident. The events at Koniuchy have been described by Chaim Lazar in Destruction and Resistance (1985) in which he claimed 300 people had been murdered. This number has not been supported by other sources. In Rich Cohen's account of a Jewish partisan unit, which describes the massacre of civilians, Koniuchy is described as a "pro-Nazi" town that was used as a staging ground for German attacks against partisans.

In a November 2008 interview with Adam Fuerstenberg, former director of Toronto’s Holocaust Centre, York University professor Sara Ginaitė, a veteran Jewish partisan fighter, described Koniuchy as having a record of hostility to the partisans and that, in collaboration with the Nazis and the local police, the town had organized an armed group to fight the partisans.

In Poland and Lithuania, the Koniuchy massacre is treated as one of the many war crimes.

The Institute of National Remembrance initiated a formal investigation into the incident on March 3, 2001, at the request of the Canadian Polish Congress. The institute examined a number of archival documents including police reports, encoded messages, military records and personnel files of the Soviet partisans. Requests for legal assistance were then sent to state prosecutors in Belarus, Lithuania, the Russian Federation and Israel.

The Lithuanian prosecutor general subsequently opened its own investigation into the massacre. As part of its investigation, Lithuanian prosecutors have sought out Jewish veterans of the partisan movement, including Ginaitė, for questioning. Also under investigation is Yitzhak Arad, a former IDF brigadier general, Jewish resistance movement veteran, and former chairman of Yad Vashem, who served as a member of a commission appointed by Lithuania's president in 2005 to examine past war crimes. Arad became the subject of criticism by Lithuanian right wing groups after his public recommendation for an examination of Lithuania's role in the Holocaust. An investigation into Arad's wartime activities in Koniuchy was opened by Lithuania's chief prosecutor in the wake of the criticisms of Arad's proposal.

In May 2004, a monument commemorating the event was erected in Kaniūkai with the names of the 34 victims.