WASHINGTON — The fighting in Gaza ended months ago, but the fight over the war rages on between Israel and NGOs.

NGOs have been issuing reports accusing Israeli of war crimes. In response, the Israeli army recently released a 163-page, 460-point account seeking to rebut such claims and discredit those making them.

At issue is the three-week Israeli invasion of Gaza starting in December 2008, launched in response to thousands of Palestinian rocket attacks against civilian targets in the south of Israel. Approximately 1,300 Palestinians were killed in the fighting, many of them militant fighters associated with Hamas, the Palestinian group in control of Gaza. But hundreds of Palestinian civilians are also believed to have been killed.

Thirteen Israelis were killed, including several civilians. Hamas rockets during the war reached as far as the Israeli cities of Yavneh, Beersheva and Kiryat Gat.

Some of the arguments between Israel and the NGOs revolve around alternating versions of the facts of the war, others address theories of the laws of war, and still others lunge with ferocity at the very legitimacy of one side or the other to even make an argument.

The stakes are high — as high as the threat of charges against Israeli officers and an effort by some Israeli officials to use the law as a weapon to limit international funding of human rights groups.

From the outset, the Israeli report cites an array of international law readings to show that Israel’s war was just. It also takes aim at what it describes as the tendency of some critics to rush to draw conclusions of national guilt from scattered evidence. “Often,” the Israeli report stated, “these leaps of logic bypass the most basic steps, such as identification of the specific legal obligation at issue and explanation of how it was violated.”

To buttress its case, the Israeli army paper cited a wealth of recommended practice from U.S., British and Dutch military manuals, as well as rulings concerning the NATO action against Yugoslavia in Kosovo in 1999; the goal was to establish that there is a legally tolerable threshold of civilian death, particularly in cases of urban warfare.

At times, the Israeli report devolves into petty sniping at critics. Meanwhile, in recent weeks, top Israeli officials smear critics with ancient guilt-by-association accusations.

It’s not much prettier on the human rights side: Reconstructions of the horrific death of civilians replete with painstakingly gathered evidence are coupled with bewildering omissions of context and blended into a package that assumes an inherent Israeli immorality.

The Israeli report repeatedly expressed frustration with efforts to turn criticism of individual officers and soldiers into a wholesale indictment of Israel’s military establishment and the decision to resort to military force.

It’s a pattern that is in evidence in three successive reports published by Human Rights Watch, perhaps the most prominent of the groups engaged by the government since the end of the war. One in March dealt with the use of white phosphorous; another in June dealt with high-precision missiles fired from pilotless drones; the most recent, earlier this month, deals with the killings of individuals bearing white flags.

Only the first report, on the use of phosphorous, chronicles what could be described as an alleged pattern of abuse.

The other two reports from Human Rights Watch focus on a relatively small number of cases: six instances of Israeli drones allegedly hitting civilian targets isolated from fighting and seven shootings resulting in 11 deaths. Still, even in those reports, Human Rights Watch uses language suggesting pervasive violations.

The HRW reports fail to assess evidence — including videos of Israeli forces holding their fire because of the presence of civilians — that Israel has provided to show that such incidents were the exception to the rule; they fail to examine what measures Israel has taken to prevent civilian deaths, which would be pertinent in examining any claim of war crimes.

Israeli officials are also guilty of omissions. The army report cites tonnage of food and medical equipment allowed into Gaza during the operation for humanitarian relief; it does not, however, translate these raw figures into proportions and fails to address claims by an array of groups — including Human Rights Watch — that Israel used humanitarian relief as leverage, and the result has been malnutrition and want.

Similarly, in describing the lead up to the war, the Israeli army provides a persuasive, blow-by-blow account of the intensification of indiscriminate rocket fire that led it to launch its invasion; but it omits any mention of the three-year siege Israel has imposed on Gaza, or that Hamas rulers in Gaza used the siege as a pretext for the rocket fire. In one line, the Israeli report states that Gaza is free of occupation, but fails to note that Israel continues to control all but one point of entry into the area.

One of the more bizarre omissions in the Israeli army report is how it deals with the deaths of 42 police cadets in a missile strike in the first days of fighting. Human rights groups allege that the police were not a legitimate target; they were recruits, drawn from the massive ranks of Gaza’s unemployed, who were “at rest” at a graduation ceremony. Moreover, they were supposedly slated for non-combat patrol roles.

The Israeli army report does not mention the strike at all, or the deaths. Instead, it spends five pages generally justifying attacks on police, and noting that in some cases terrorists have doubled as police –although groups, including B’Tselem, have proffered evidence showing that this was precisely not the case in the matter of the cadets.

Israeli spokesmen also repeatedly question the reliability of the human rights reports, saying witnesses must be compromised by fear of Hamas retaliation. “Human Rights Watch is relying on testimony from people who are not free to speak out against the Hamas regime,” Mark Regev, the prime minister’s spokesman, told the BBC on Aug. 13. In fact, HRW attempts to get witnesses alone, and corroborates their accounts with medical examinations and forensic evidence.

Israeli government spokesman, moreover, do not account for the fear of retaliation — albeit of a less lethal kind, involving social ostracization — when they dismiss accounts of atrocities compiled from soldiers by groups such as Breaking the Silence.

Then there are the examples where facts simply diverge: Israel says it used white phosphorous as an obscurant when it faced Hamas anti-tank forces; human rights groups have alleged that the presence, in some cases, of armed forces was minimal and did not justify the use of the phosphorous, which upon skin contact may maim and kill. Israel says the number of civilians killed numbered in the low hundreds; human rights groups place it at closer to 1,000.

Some divergences have to do with the perspective of the claimant. The Israeli army report says warnings to civilians to leave an area were as precise as they could be without betraying tactics and putting soldiers in danger; Human Rights Watch says the warnings, while welcome, were often too generalized and even confusing.

Such differences might have been addressed by dialogue and an exchange of information that would observe limits aimed at preserving Israeli tactical secrecy. Israeli officers, for instance, have said that they have names to attach to fatalities that show that the vast majority were combatants; but they have not provided these to human rights groups.

Human rights groups have constantly pressed Israeli authorities to address specific claims, and have been brushed off. Yet the release of information that at least 13 incidents were under criminal investigation prior to the July 29 publication date of the military’s report might have gone some way toward refuting claims that Israel was cavalier about abuse allegations.

Instead, Israeli officials have devolved into name-calling, backed by an array of pro-Israel NGOs and lobbying groups that distribute — sometimes anonymously — “backgrounders” that attempt through sometimes tenuous links to discredit the human rights groups.

More substantively, Prime Minister Benjamin Netanyahu’s government is now seeking ways to legally cut off foreign government funding for Israeli human rights NGOs.

The human rights groups are not above using the law to make an exception of Israel; HRW frequently calls for international investigations, saying that Israel has repeatedly failed “to conduct credible investigations into alleged violations of the laws of war.”

The problem with such calls is that Israel believes such international mechanisms cannot be trusted because they are wrapped into the United Nations — a worry Human Rights Watch admits is credible.

Israeli army spokesmen say it is fairer to note what Israel is doing to prevent the recurrence of abuses, citing as an example the introduction of the ultra-precise missiles.