Officials laid wreaths at a memorial to victims of the Ustashe puppet regime, which incarcerated Jews, Serbs and others in brutal conditions.
However, the service at Jasenovac was boycotted by Jewish and Serb groups.
They say the new Croat government has not acted against renewed use of Ustashe salutes by nationalists.
In January, ultra-nationalists shouted pro-Nazi slogans at a rally attended by thousands of people, including Deputy Parliamentary Speaker Ivan Tepes.
Similar slogans were also chanted during a football match between Israel and Croatia in March, attended by Prime Minister Tihomir Oreskovic.
Croatia's Jewish community held a separate Holocaust commemoration a week ago.
Mr Oreskovic and President Kolinda Grabar-Kitarovic both voiced regret over the boycott.
Earlier this month they explicitly condemned the Ustashe regime's crimes for the first time during a visit by Nicholas Dean, the US State Department's special envoy for Holocaust issues.
Three-quarters of about 40,000 Croatian Jews were killed by the Ustashe and Jews now make up less than 1% of the population.

Wright picked up the injury against League Two leaders Northampton Town on Tuesday and was replaced by Chey Dunkley for the final 14 minutes.
"It looks like a grade one tear to his hamstring, which rules him out for around 10 days to start with," manager Michael Appleton told BBC Radio Oxford.
"It's a blow from a playing point of view and also because he's a leader."
Wright, 29, has made 30 appearances in all competitions for Oxford this season.
On Saturday they host fourth-placed Accrington, who are six points behind Appleton's side with two games in hand.
Croatia has held a memorial service for tens of thousands of people murdered by Nazi Germany's allies at the Jasenovac death camp.
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Oxford United captain Jake Wright is set to be out for three to four games with a hamstring tear.