Publication of the list of groups from Europe, the United States, Chile and South Africa follows legislation in March banning entry to foreigners who support boycotting the country or its settlements, which are seen as illegal under international law.
Rights groups criticised the law as "thought control" and noted that Israel also controls who enters the Palestinian territories apart from one border crossing between the Gaza Strip and Egypt.
"We have moved from defence to attack. The boycott organisations need to know that the state of Israel will act against them and will not allow them to enter its territory in order to harm its citizens," Public Security and Strategic Affairs Minister Gilad Erdan wrote in a Hebrew-language statement.
Among the banned groups are the Paris-based Association France Palestine Solidarite, British charity War on Want and the American Friends Service Committee - a Nobel Peace Prize-winning US Quaker organisation.
South African, French, Italian and Chilean branches of the Boycott, Divestment and Sanctions movement (BDS) also featured on the blacklist.
The statement from Erdan's office said that the proscribed NGOs were "the main boycott organisations which operate consistently and continuously against the state of Israel, while putting pressure on organisations, institutions and countries to boycott Israel".
It said that they employed "a false propaganda campaign aimed at undermining Israel's legitimacy in the world".
At a meeting in Jerusalem on Sunday with Norwegian Foreign Minister Ine Eriksen Soreide, Israeli President Reuven Rivlin told her that the boycott movement did nothing for the cause of peace.
"I believe that BDS leads to increasing hatred," his office quoted him as saying in English.
"It symbolises all that stands in the way of dialogue, debate, and progress," he added.
The Palestine Group of Norway was among the groups named on Sunday.
In November, Israel denied entry to a US employee of Amnesty International as part of its anti-boycott offensive.
Amnesty and Israeli officials said at the time that Raed Jarrar, an advocacy director for the Middle East and North Africa at the rights group, was prevented from entering the occupied West Bank.
Jarrar was turned back by Israeli authorities at the land crossing between Jordan and the West Bank.
Amnesty did not appear on Sunday's list.
Israeli authorities said Jarrar was barred at Erdan's orders over unspecified links with BDS.
Israel sees the boycott movement as a strategic threat and accuses it of anti-Semitism - a claim activists deny, saying they want only to see an end to Israel's occupation.
