A storm is brewing in Israel over the Israel Defence Forces' (IDF) chief rabbi's opposition to women serving in the armed forces, with politicians and pundits alike calling for his head in the wake of the controversy. Rabbi Avichai Rontzki's stance is based on his interpretation of Jewish law, which cuts little ice among secular sectors of Israeli society – many of whom express growing concern that the army is falling into the clutches of the national religious camp.

According to Haim Oron, leader of the New Movement-Meretz party:

Rontzki's comments highlight the trend where instead of religious Zionism adopting the values of the IDF and the country, the IDF and country are adopting the values of religious Zionism, in its nationalist and orthodox version. If this trend continues, the IDF may be transformed from an army of the people to Phalangists carrying religious artefacts.

His fears are not as far-fetched as they may appear to those who still view the IDF as a broadly secular state institution. During Operation Cast Lead, soldiers were issued with pamphlets from IDF chaplains that attempted to paint the conflict as no less than a holy war being waged on behalf of world Jewry. A friend of mine who was deployed to the Gaza border showed me one such leaflet, in which troops were told they were "fighting a war for the Jewish people", rather than on behalf of all Israel's citizens.

"I thought 'what would a Bedouin soldier make of such statements?'," he said. "The Bedouin soldier would be there to stop rockets falling [on his homeland], not to fight God's war." The jihadist bent of such propaganda is another sign of the "army's shift to the right", he explained. Statistics bear out his assertion, with 20% of officers hailing from national religious backgrounds, proportionally much higher than the make-up of the general population.

One senior IDF officer attributes the figures to the attitudes to army service among the national religious community versus those of the more secular populace. "The national-religious are replacing the kibbutzniks in the ranks of combat and command," he said. "They learn at home the importance of sacrifice for the nation and of giving of themselves for the state."

While most ultra-orthodox Israelis still refuse to send their children to the army, those from the national religious camp have no problem with their offspring serving the state in such a fashion; in fact, such a display of commitment to the country is endemic to the nationalist element of their communal politics.

At ground level the influx of soldiers adhering to religious laws and principles is not necessarily a bad thing for those against whom the troops are operating, since their strict observance of Jewish law requires them to behave in a more humane fashion than many of their less religious peers often do. However, on a wider level, the discord between religious and military leaders' stance towards Israeli policy places observant soldiers in a quandary when it comes to implementation of certain strategies.

A case in point was the Disengagement of 2005, when many of the religious members of my brigade refused to participate in the evacuation of the settlement of Homesh in which we assisted. Soldiers from settler backgrounds, as well as those simply ideologically opposed to the move, were treated with kid gloves by commanders anxious to avoid an internal confrontation, rather than dealing with their insubordination in accordance with army guidelines.

By backing down and allowing external factors to disrupt the regular chain of command, a precedent was set that is likely to come back to haunt the IDF if any similar withdrawal from the West Bank is attempted in the coming years. Settler leaders have been whipping their followers into an ever-growing frenzy ever since the first Disengagement, and their fighting talk acts to dampen the ardour of any politician or military strategist considering such a move, despite believing it to be in the long-term interests of Israeli security. The divergent paths taken by the state's leaders and the national religious hierarchy in terms of ceding land raises the very real prospect of a mass mutiny within the ranks of orthodox troops, and must not be overlooked by those with an interest in the stability of the region.

Much is made by the Israeli right of hostile forces having been co-opted into a wider religious war; with Islamic Jihad, Hamas and al-Qaida militias regularly held up as proof that Israel's enemies cannot be placated via negotiations or concessions. Those groups' religious convictions are, they assert, intractable to the point of no return, and the only way to fight against such intransigence is through the sights of a gun.

However, the same characteristics can, and should, be ascribed to a growing section of the IDF, especially in the wake of statements such as Rontzki's, as well as the military rabbinate's crusader stance during Cast Lead. On one level, Rontzki's "chauvinistic and patronising" attitude towards female soldiers can be easily dismissed as the ranting of a man utterly stuck in the past, who refuses to accept that the world has progressed past the patriarchal atmosphere prevalent in biblical times. But far more worrying is the fact that such backward-thinking fundamentalists should be permitted so much leeway to spread their influence among the country's soldiers, and afforded such positions of power within the IDF. Religious dogma has no place in such an institution; to allow such corrosive and dangerous thinking to pervade as sensitive an arena as Israel's armed forces is simply a recipe for disaster.