In 2009, he published a book (The King's Torah) in which he writes that it is permissible for Jews to kill non-Jews (including children) who threaten the lives of Jews. The book states "There is a reason to kill babies [on the enemy side] even if they have not transgressed the seven Noahide Laws because of the future danger they may present, since it is assumed that they will grow up to be evil like their parents." They can be killed indirectly to put pressure on enemy leaders, or if they are "in the way". They can also be harmed if they "prevent a rescue, because their presence contributes to murder". He also writes that children of the king can be harmed to pressure him if he is wicked and harming them will prevent him from acting wickedly. He adds that "it is better to kill one pursuing another to murder him, than to kill others." The book was distributed by Yeshivat HaRaayon HaYehudi in Jerusalem, which adheres to the ideas of the late Rabbi Meir Kahane.
Yehuda Bauer described the book as a "mortal danger to the Jewish people as a whole". Ophir Paz-Pines, a member of the Israeli Knesset, called on the attorney general to open a criminal investigation against Shapira on account of the book.
Shapira was detained for questioning in 2006 over an article that advocated expelling or killing all male Palestinians above the age of 13 in the West Bank. In 2008 he signed a "manifesto" in support of Israelis suspected of beating two Arab youths during that year's Holocaust Remembrance Day. In January 2010, he was arrested for his "alleged involvement in the torching of a Palestinian mosque in the village of Yasuf." He denied any involvement, and was released due to lack of evidence.
In October 2010, he urged Israel Defense Forces soldiers to use Palestinian civilians as human shields, claiming that it was against "true Jewish values" for a soldier to endanger his life for the sake of enemy soldiers or civilians.
- Matthew Wagner, "Shimshon soldiers to be hailed at 'farbrengen'", Jerusalem Post, 12 November 2009
- Jonathan Lis, "Court frees Od Yosef Chai Yeshiva head Rabbi Yitzhak Shapira", Jerusalem Post, 29 January 2010
- "Rabbi's book says Jews can kill gentiles", Jewish Telegraphic Agency, 9 November 2009
- Roee Sharon, "'ספר שמופץ בימין מסביר מתי מותר להרוג 'גויים" Ma'ariv, 9 November 2009
- Matthew Wagner, "Shapira's distinction between Jewish, gentile blood", Jerusalem Post, 2 January 2010
- Chaim Levinson, "Police release rabbi arrested for inciting to kill non-Jews", Haaretz, 27 July 2010
- Roy Sharon, " Police release rabbi arrested for inciting to kill non-Jews ", Maariv, September 11, 2009
- Matthew Wagner, "Book advocating killing gentiles who endanger Jews is hard to come by", Jerusalem Post, 11 November 2009
- Yehuda Bauer, "The racist teaching of the extreme right", Maariv, 11 March 2011
- ירן דנש ומרב דוד, "פינס למזוז: פתח בחקירה נגד הרבנים שהסיתו", Maariv, 9 November 2009
- Matthew Wagner, "West Bank rabbi, activist arrested", Jerusalem Post, 12 September 2006 
- Uri Blau and Yuval Azoulay, "Violence follows removal of trailer from West Bank outpost", Haaretz, 27 July 2008
- "Rabbi arrested, suspected in West Bank mosque arson", BBC News, 27 January 2010
- 'IDF to blame for price-tag atmosphere'
- Matthew Wagner, "Religious Affairs: Caught in the crossfire", Jerusalem Post, 13 March 2008