Leaders of some of Israel’s most prominent human rights organizations say they are working in an increasingly hostile environment and coming under attack for actions that their critics say endanger the country.

The pressure on these groups has tightened as the country’s leaders have battled to defend Israel against accusations of war crimes, the rights advocates say, raising questions about the limits of free speech and dissent in Israel’s much vaunted democracy.

“Over the years, in a variety of international arenas,” said Hagai El-Ad, executive director of the Association for Civil Rights in Israel, “it was key for Israeli officials to say, ‘Yes, there are many problems, perhaps even abuses; however, we have a strong, vibrant civil society with a plethora of voices and we are very proud of that.’

“It is inconsistent to make those statements and at the same time create a situation that colors us as traitors in the public eye.”

Governments and the watchdog organizations that monitor them have rarely seen eye to eye. But rights advocates say that to many conservatives and leaders of Israel’s right-leaning government, the allegations of war crimes against the Israeli military that followed the Gaza war in the winter of 2008-9 have turned human rights criticism into an existential threat that is chipping away at the country’s legitimacy. And officials have been blunt in their counterattacks.

The chief catalyst was the United Nations report last fall on the war in Gaza, by a fact-finding mission led by the South African jurist Richard Goldstone. The report accused Israel and Hamas of possible war crimes.

Prime Minister Benjamin Netanyahu has since identified what he calls the “Goldstone effect,” meaning the delegitimization of Israel abroad, as a major strategic threat.

Last summer, he attacked a leftist organization, Breaking the Silence, that published allegations by unnamed Israeli soldiers about human rights violations during the war, as selectively anti-Israel.

Some international rights groups that have been critical of Israel, like Human Rights Watch, have said Israel’s government was “waging a propaganda war” to discredit them. A senior Netanyahu aide affirmed in an interview last year that Israel was “going to dedicate time and manpower to combating these groups.”

Israeli rights advocates say that such comments by officials have fostered an atmosphere of harassment. While they do not accuse the government of orchestrating a campaign against them, they point to a number of seemingly unconnected dots that they say add up to a growing climate of repression.

In Sheikh Jarrah, the East Jerusalem neighborhood where several Palestinian families have been evicted from their homes and replaced by Jewish settlers, the police have arrested dozens of Israelis attending peaceful protests in recent months. Mr. El-Ad was detained for 36 hours in January, along with 16 other activists, after he explained to the police that their decision to break up a rally had no legal grounds. One organizer of the protests was arrested at his parents’ Jerusalem home on a night in late March, and released three days later.

Sari Bashi, the director of Gisha, an advocacy group that focuses on freedom of movement for Palestinians, said her organization was harassed last year by the Israeli tax authorities. She said they questioned why Gisha should be tax exempt when that status was meant for organizations that promoted the public good. Eventually, she said, the authorities backed down.

Then an ultra-Zionist nongovernmental organization called Im Tirtzu (Hebrew for ‘If you will it’ — the first part of Theodor Herzl’s famous maxim) attacked a major organization, the New Israel Fund, which channeled about $29 million to Israeli groups in 2009, including some Arab-run, non-Zionist groups. The fund describes itself as pro-Israel and says it does not agree with all the positions of the groups it helps, but it supports their right to be heard.

Im Tirtzu published a report in January asserting that 92 percent of the quotes from unofficial Israeli bodies supporting claims against Israel in the Goldstone report were provided by 16 nongovernmental organizations financed by the New Israel Fund.

The New Israel Fund dismissed Im Tirtzu’s findings as a fabrication, saying most of the references it cited had nothing to do with Gaza during the Israeli offensive.

Still, for three weeks, Im Tirtzu plastered billboards across the country with posters featuring a crude caricature of the New Israel Fund president, Naomi Chazan. The posters depicted her with a horn attached to her forehead (in Hebrew, the word for fund also means horn) and bore the legend “Naomi Goldstone Hazan.”

Perhaps the most alarming sign to rights advocates was a preliminary vote in Parliament supporting a bill that called for groups that received support from foreign governments to register with Israel’s political parties’ registrar, which could change their tax status and hamper their ability to raise money abroad. It swept a preliminary vote in the 120-seat Parliament in February with 58 in favor and 11 against.

Proponents say the bill is needed to improve transparency. “Up until now they have enjoyed a halo effect as highly regarded human rights watchdogs,” said Gerald Steinberg, an Israeli political scientist and president of NGO Monitor, a conservative watchdog group financed by American Jewish philanthropists. “They were not seen as political organizations with biases and prone to false claims. Now, they are coming under some kind of scrutiny.”

But rights organizations say that they are already required to list publicly the sources of their funding, and that the bill is actually intended to stifle dissent.

Right-wing organizations like those encouraging Jewish settlement in Arab areas of East Jerusalem receive the overwhelming share of their financing from individuals and philanthropies whose identities are often not disclosed.

For now, the bill has effectively been blocked until its proponents reach agreement with the Labor ministers in the governing coalition, who are trying to water it down.

But Ms. Chazan said the bill could not be finessed.

“This law has to disappear,” she said. “It is the single most dangerous threat to Israeli civil society since its inception.”

For Ms. Chazan, a vibrant and diverse civil society is the bedrock of Israeli democracy, and what being Israeli is all about. “We love this country and we want it to be decent,” she said. “We believe the more decent Israel is, the better chance it has of surviving.”

But Mr. Steinberg says that organizations like the New Israel Fund, with their deep pockets and multiple petitions to Israel’s Supreme Court, have “distorted the marketplace of ideas.”

“Part of what is going on now,” he said, “is a sense that this is getting out of control.”