Pope Francis has paid tribute to Lithuanians who suffered and died during Soviet and Nazi occupations on the day the country remembers the near-extermination of its Jewish community during the Holocaust.

Francis began his second day in the Baltics in Lithuania's second city, Kaunas, where an estimated 3,000 Jews survived out of a community of 37,000 during the 1941-1944 Nazi occupation.

During Mass in the lush Santakos Park under a brilliant autumn sun, Francis honoured both Jewish victims of Nazi-era executions and the Lithuanians who were deported to Siberian gulags or were tortured and oppressed at home during five decades of Soviet occupation.

"Earlier generations still bear the scars of the period of the occupation, anguish at those who were deported, uncertainty about those who never returned, shame for those who were informers and traitors," Francis told the crowd.

"Kaunas knows about this. Lithuania as a whole can testify to it, still shuddering at the mention of Siberia, or the ghettos of Vilnius and Kaunas, among others."

He denounced those who get caught up in debating who was more virtuous in the past and fail to address the tasks of the present – an apparently veiled reference to historic revisionism that is afflicting much of Eastern Europe as it comes to terms with the Holocaust.

Holocaust Memorial Day: three unsung heroes who helped Europe's Jews escape the Nazis

The issue is acute in Lithuania, where ordinary Lithuanians executed Jews alongside the Nazi occupiers, wiping out the Jewish population of the capital of Vilnius that was known for centuries as the "the Jerusalem of the North" because of its importance to Jewish thought and politics.

Francis is to continue the remembrance with a visit to a museum in Vilnius that is dedicated to Soviet atrocities as well as a prayer in the Vilnius Ghetto, which 75 years ago was finally destroyed and its remaining Jewish residents executed or sent off to concentration camps.

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Each year, the 23 September anniversary of the destruction of the Vilnius Ghetto is commemorated with readings of the names of Jews who were executed by Nazis as well as by complicit Lithuanian partisans in the nearby Ponary forest.

Francis is travelling to Lithuania, Latvia and Estonia to mark their 100th anniversaries of independence and to encourage the faith in the Baltics, which saw five decades of Soviet-imposed religious repression and state-sponsored atheism.

Lithuania is 80 per cent Catholic; Lutherans and Russian Orthodox count more followers in Latvia and Estonia, where Francis visits on Monday and Tuesday.

The Baltic countries declared their independence in 1918 but were annexed into the Soviet Union in 1940 in a secret agreement with Nazi Germany. The Vatican and many Western countries refused to recognise the annexation. Except for the 1941-1944 Nazi occupation, the Baltic countries remained part of the Soviet Union until its collapse in the early 1990s.