A judge in the city of Oryol found Dennis Christensen, 46, guilty of "organising the activity of an extremist organisation". He called on Russian Federation to respect freedom of religion, and said the ministry would assist Christensen if he chose to appeal.
It has been suggested that Jehovah's Witnesses are under suspicion because they are seen as a Western influence, too independent from the Russian government, and activists are concerned that the crackdown is a test to see how Russians will react.
A judge at the district court said the six years in a penal colony was a "minimal sentence", local news site Oryol Novosti reported.
Dennis Christensen was arrested in May 2017 after a police raid on his congregation just south of Moscow.
Now, almost 100 members of the group face charges in Russian Federation and more than 20 of them are in jail awaiting trial, according to the AFP.
Christiansen had pleaded innocent, saying he was exercising freedom of religion guaranteed in Russia's constitution.
Mr Christensen told the court last week that he was being persecuted "for being a religious believer who loves his neighbour as himself". Almost 100 of the church's members face charges and there are now about 20 members in prison and awaiting trial.
He said: "In essence we have returned to Soviet times".
The Danish foreign minister, Anders Samuelsen, called on Moscow to respect religious freedom and criticised it for classifying Jehovah's Witnesses as a terrorist group.
Kremlin spokesman Dmitry Peskov said that there had been reasons for Christensen's arrest, but that he was unaware of the details of the case.
"The man was sentenced to six years behind bars, because he, along with others of the same religious beliefs, read the Bible and spread their religious views", Bogdanov said.
Anton Bogdanov, Christiansen's lawyer, said he planned to appeal Wednesday's verdict, which he termed illegal and feared would set a risky precedent. "It is sad that reading the bible, preaching, and living a moral way of life is again a criminal offense in Russia", Sivulskiy said in a public statement on Wednesday.