The Israeli general in charge of most of the West Bank has a message for members of Congress who want to end American aid to the Palestinian Authority because of its bid to join the United Nations: Don’t do it.

Brig. Gen. Nitzan Alon, commander of the Judea and Samaria Division, said that such a step would lead to instability and insecurity for both Palestinians and Israelis.

“Stability in the region includes the ability of the Palestinian Authority to pay its salaries,” General Alon said this week in a rare on-the-record interview, reflecting a consensus among Israeli defense officials. “Reducing the Palestinians’ ability to pay decreases security. American aid is relevant to this issue.”

The position of both the White House and a number of American legislators is that the only path to Palestinian statehood is through direct talks with Israel. The Obama administration has promised to veto the recent Palestinian bid for recognition by the United Nations Security Council, but some legislators — Republicans and Democrats — want to go beyond that and cut off the hundreds of millions of dollars that Congress allocates annually to the Palestinian Authority.

General Alon, a former commando and intelligence officer who is scheduled to end his command after two years in his post, agreed to discuss issues that have arisen during his tenure. In a wide-ranging conversation, he brought up American aid and spoke with great concern about increasing violence by radical Israeli settlers, which he called “Jewish terrorism.” “We should do much more to stop it,” he said.

He called for more police officers and for getting them to shift some focus from their main mission of protecting settlers to stopping radicals. The army has sent some troops in for this.

General Alon said violence was a problem in both directions. He said Palestinian rock-throwing had increased since the Palestinian president, Mahmoud Abbas, went to the United Nations last month, leading to the deaths of a settler and his infant son whose car turned over after they were pelted. In recent months, the militant settlers have burned several mosques and destroyed acres of Palestinian olive and fig trees. Last week, dozens of settlers surrounded an Israeli Army vehicle and assaulted soldiers.

On General Alon’s desk sits a two-screen computer. During the interview, one showed in real time the deployment of security forces around settlements where Palestinians were picking olives. The other showed a news site of the Israeli settler movement.

Every year, the olive harvest produces increased tension because some of the trees are next to —or inside of — Israeli settlements.

“We have taken it as a mission to make sure the harvest goes well this year,” an Israeli colonel, speaking under normal military rules of anonymity, said by telephone. “We’re using more troops.” The army is allowing Palestinians a much shorter time to harvest olives this year — dropping to about two weeks from five — and is guarding the process more closely.

The colonel said that cooperation with the Palestinian Authority was good. But some Palestinian officials said the opposite.

“The soldiers never help us,” Ghassan Douglas, the Palestinian official who monitors Israeli settlements in the Nablus region, said in an interview. And Ghassan Khatib, a spokesman for the Palestinian Authority, charged in a statement that soldiers “protect the settlers while they are carrying out these illegal crimes.”

There is clearly a public-relations battle under way. Most of the world shares the Palestinian position that the settlements are illegal and illegitimate, so anti-settler agitation is seen as less offensive than anti-Palestinian activity. Even within Israel, some of the more radical settlements are seen as politically costly.

A spokesman for the United Nations human rights commissioner said on Tuesday that the Israeli Army was not doing enough to protect Palestinians.

“The accountability for settler violence against Palestinians is less than adequate, let’s say, and certainly not comparable to the reverse cases,” the spokesman, Rupert Colville, said at a news conference in Geneva.

Though the relationship between the Israeli Army and the Palestinian security forces has been complicated, over the past three years, calm has largely prevailed over the West Bank. Palestinian forces mostly control about 40 percent, Israelis the rest.

But even the 40 percent, where most Palestinians live, is subject to nightly raids. General Alon said that a few years ago, Israeli troops went into the West Bank more than a dozen times a night, but that is down by half now. Fewer, he said, would require a political decision. The Palestinian Authority says the raids harm — and sometimes kill — their citizens and humiliate their forces.

But General Alon said the current rate of intervention was required to maintain intelligence dominance. He gave as an example the recent arrest of two men accused of throwing the rocks that caused the car crash that killed the settler and his son. The Israelis went into the village of Halhoul themselves because, he said, they were afraid to compromise certain intelligence sources and worried that the Palestinians would not make the arrests.

General Alon said that the effectiveness of the Palestinian security forces depended on how they were seen at home.

“As long as they see them as patriots working to build a Palestinian state, they will be able to keep working with us,” he said of the Palestinian forces. “If there is no political horizon, cooperation is endangered.”

General Alon also said that the role of Israeli forces had to be limited. “We can’t do our mission only with military tools,” he said. “Diplomacy and economy are very relevant.”

Prime Minister Benjamin Netanyahu and his aides have said they are reluctant to withdraw from the West Bank because they say that when Israel withdrew from Gaza in 2005 Hamas took over and stepped up rocket fire against Israel. Having the same thing happen so close to Tel Aviv would be unacceptable, they say.

General Alon said that what happened in Gaza should be a lesson, “but not cut and paste,” meaning that a withdrawal was possible but would require thoughtful adjustments.

He pulled a book from his drawer. As a goodbye present, General Alon said, he was giving his staff a Hebrew translation of “Why Don’t We Learn from History?” by B. H. Liddle-Hart. It argues, among other things, that “truth is a spiral staircase. What looks true on one level may not be true on the next higher level.”