After years of rabbinate control of religious divorces, the ministry said the judiciary was going to get involved in order to "liberate" women.
Hundreds or even thousands of women in Israel have been prevented from rebuilding their lives as they require the permission of their husbands to get a divorce.
In Israel, only a rabbinical court can seal a marriage or divorce, as civil marriage does not exist.
The ministry issued an order for the civil judiciary to prosecute men who refuse to grant permission for divorce -- through what is known as a "get" -- after a rabbinical court orders it.
Without a "get", a woman is known in Hebrew as "agunot" and remains bound to her husband and unable to remarry.
There are currently 131 such women in Israel for an average of 11,000 divorces of Jewish couples each year, according to the director of rabbinical courts, Shimon Yaakobi.
If she has a child with another man, he will never be able to marry, under Jewish law.
But this figure is only a tally of women for whom religious justice has ordered the husband to accept divorce.
Aliza Gellis, head of the Yad L'isha centre that provides legal aid to women stuck in hopeless marriages, said her organisation gets 6,000 requests for assistance each year.
"When a rabbinical court decides to force the man to give the get or the woman to receive it, it is necessary to envisage the opening of a criminal investigation against the recalcitrant person and to charge him if need be," said the ministry.
"He who refuses to give the get deprives his wife of her freedom and prevents her from rebuilding her life," it said in a statement.
Faced with recalcitrant cases, rabbinical courts can seize driving licences, issue bans on travel abroad or block bank accounts.
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