Motorists exited their vehicles and students at schools stood in ceremonies beginning with the 10:00am (0700 GMT) siren.
The main ceremonies in the country will take place at Jerusalem's Yad Vashem Holocaust memorial, with Israeli Prime Minister Benjamin Netanyahu and other officials attending.
"Today, too, there's an extremist regime that's threatening us, threatening the peace of the entire world", Netanyahu said of Iran.
In addition to noting that 6 million Jewish men women and children were killed in the Holocaust, the proclamation states that millions of other Europeans were murdered by the Nazi regime including Roma and Sinti Gypsies, mentally ill and physically deformed individuals, Slavs and other minorities, Christians, Jehovah's Witnesses, gays and political dissidents.
'I have a message to the rulers of Iran - don't test Israel's resolve'.
On Wednesday, President TrumpDonald John TrumpWoman "dabs" as Trump signs sex trafficking bill Graham uses Fox News appearance to ask Trump not to fire Mueller Trump's Syria tweet surprised WH staff working on response to chemical attack: report MORE declared April 12 through April 19 to be Days of Remembrance of Victims of the Holocaust to honor the member of victims of Nazi persecution. Our hearts were rent by the horrific sights. These aren't empty words, we back them up with action'.
Mr Netanyahu compared the 2015 nuclear deal between world powers and Iran to the appeasement of Adolf Hitler in the run-up to the Second World War. He said the agreement "released the Iranian regime from its chains and since has devoured country after country, similar to what happened in Europe in the 1930s".
On the eve of the Remembrance Day, shops and restaurants closed down while television and radio stations broadcast programmes about the Holocaust.
Holocaust survivors lit six torches at the Wednesday memorial to mark the six million Jews massacred by the Nazis during World War II.
Dignitaries laid wreaths at Yad Vashem, the national Holocaust Memorial in Jerusalem.
Also, while the vast majority of historians believe that approximately six million Jews were exterminated in the Holocaust, almost one-third of all Americans (31%) and more than four-in-ten Millennials (41%) believe that only two million Jews or fewer were killed in the Holocaust. Israel was established afterward in 1948, and hundreds of thousands of survivors fled to the Jewish state.