He was reluctant to speak about Estonia's recent decision to remove a Soviet-era war memorial which riots by mainly Russian-speaking Estonians - a significant minority of 300,000 in the country of 1.3 million.
But he said, on Thursday, it had been a sensitive issue for Jews living in Estonia as many were Russian-speaking war veterans.
The new synagogue was built at a cost of about $2 million with money from the US-based Rohr family foundation and Estonian Jews and non-Jews.
It will fit 180 people in the main worship area.
The Jewish population of Estonia is about 3,000.
'Free of Jews'
Estonia, with its small population, was the only country in Europe to be declared "free of Jews" by the Nazis.
Before the war about 5,000 Jews lived in Estonia, mostly in Tallinn. Many fled to the Soviet Union and those that remained were murdered by Nazi forces, including the last rabbi.
The last synagogue, built in 1883, was destroyed in the war during the Soviet bombing of Tallinn.
"Just like people need an apartment to live in, they also need an apartment for their soul. My wish is that every single Jewish person in the country will feel this is their home," Kot, 30, said.
Until now Estonian Jews have used a makeshift prayer room in a building next to the new synagogue.
Kot saw the synagogue as a sign of survival and tolerance and was positive not only for Jews but for the whole of Estonia.
"This is the right answer to fascism, communism and Nazism," he said.
"The communists tried wanted to kill Jewish life and the Nazis wanted to kill Jewish bodies."
Officials from the Estonian and Israeli government will attend the opening of the new building.