Air Force Commander Dan Halutz was quoted in an Israeli newspaper as saying the pilots would be treated “in the same way as the IDF (military) has dealt with refuseniks until now”.
Israeli servicemen can be jailed for refusing to carry out orders.
On Wednesday, 27 reserve pilots submitted a petition to Halutz saying they were no longer prepared to take part in missions they said were “illegal and immoral”.
Halutz replied to the pilots in a harsh letter in which he accused them of having “shoved a knife in the back of combatants”, according to an Israeli military source.
Israel has killed 12 Hamas activists in air strikes since August. Civilian bystanders have also been killed in the attacks.
A military spokesman said 20 of the signatories were no longer even attached to units flying such missions but they will be grounded.
Israeli Prime Minister Ariel Sharon also warned the pilots not to become embroiled in politics.
“This is a very severe matter which will be dealt with soon and appropriately,” he said.
One of the pilots, whose name was given only as Alon, told an Israeli daily that he felt like he had “come out against his family”.
“I was proud to belong to the organisation called the Israel Air Force and today I am ashamed”
“I was proud to belong to the organisation called the Israel Air Force and today I am ashamed,” said the Black Hawk helicopter captain.
“This is an organisation that carries out actions that in my eyes are immoral and patently illegal. It is an organisation that has no qualms about dropping bombs – it doesn’t matter if they are 250, 500 or 1000kg – on the densest neighbourhoods in the world, causing massive killing of civilians,” he said.
Alon said he would be prepared to fly missions which carried the possibility of killing civilians if he felt it was vital to Israel’s survival.
“This is not the situation in Israel 2003. We are not in a war for our existence,” he said.
“We are in a war for continuing the occupation in the territories. And in light of this dubious goal, I am not willing to be the murderer of innocent civilians.”
Former Air Force Commander Major General Amos Lapidot said that while the pilots were in a minority their unease was widely shared.
And in January last year, 52 army reserve officers and soldiers said they were refusing to serve in the occupied West Bank and Gaza.
But Major General Nati Sharoni, the military’s former head of planning, said the pilots had no right to air their grievances in such an open manner.
“Anyone who serves in the armed forces, whether active or reserve, cannot, should not, must not say this is something that I am not going to do, even if it’s questionable,” he said.
“One has to realise this is not a democratic organisation,” said Sharoni.