B'Tselem published adverts on Friday in local papers putting 10 questions to Yaalon about the army's rules of engagement in the occupied territories.
It questioned the lack of accountability and inconsistent punishment handed down to troops for killing civilians.
"Do you intend to resign?" read the last question.
B'Tselem also asked Yaalon: "Is it true that there are 'zones of destruction' in the Gaza Strip where the army receives orders to kill anyone if even that person does not endanger the lives of soldiers?"
The media campaign came a few days after an Israeli military court indicted an army officer accused by his own soldiers of emptying his weapon into a Palestinian schoolgirl who was already dead.
The charges were levelled just five weeks after the soldier was cleared of any wrongdoing in another army investigation.
Channel Two broadcast a conversation between the officer and other troops recorded on military radio at the time of shooting, where he said: "Anything that's mobile, that moves in the zone, even if it's a three-year-old, needs to be killed."
"is it true that there
are 'zones of destruction' in the Gaza Strip where the army receives orders to kill anyone if even
that person does not endanger the lives
Israeli human rights group
The rights group also asked Yaalon why "at least 1369 unarmed Palestinian civilians were killed by soldiers since the beginning of intifada when only 22 troops were accused of illegally firing and one actually charged?"
It said 529 children were among those killed civilians.
More than 3550 Palestinians - armed and unarmed - and 961 Israelis have been killed since the start of the Palestinian uprising in late September 2000, according to an AFP count.
"This is the first time we publish such adverts because the situation has become unbearable and the number of civilian deaths has steadily soared without any serious army investigation," B'Tselem spokeswoman Sarit Michaeli said.