Palestinian Authority forces clashed with Hamas militants in the West Bank early on Sunday, leaving six dead in the bloodiest such encounter in two years.

The violence erupted days after the Palestinian president, Mahmoud Abbas, assured President Obama in Washington that his troops were imposing order on the area. In Gaza, Hamas reacted by arresting Fatah activists and hinting of further revenge.

The clashes and threats show that Fatah, which dominates in the West Bank, and Hamas, which runs Gaza, remain in a tense standoff, and that the Palestinian unity needed for creation of a state is far off. Both sides said unity talks mediated by Egypt were imperiled.

A spokesman for Mr. Abbas’s West Bank forces, Adnan Dameiri, told a news conference in Ramallah that a patrol in the city of Qalqilya had come under fire on Saturday night from a house, leading to a curfew and negotiations lasting for hours. During the negotiations, a grenade was thrown from the house, killing three security officers, Mr. Dameiri said. Palestinian Authority forces then stormed the house, and two Hamas militiamen, including one of its leaders, were killed, along with the owner of the house that the militants had commandeered.

He said weapons and documents were found on the men, and added that the Palestinian Authority forces had found similar caches in recent months. Some 200 Hamas-affiliated men are in jail in the West Bank awaiting trial, Mr. Dameiri said, but he insisted that they were charged with specific violations, not for Hamas affiliation.

“In the last two years, we have proved our ability to impose law and order,” Mr. Dameiri said at the news conference. “We will continue our campaign to dismantle armed groups.”

Hussein al-Sheikh, a West Bank Fatah leader, told Israel Radio: “Whoever wants now to come in and disrupt the security and order of the Palestinian residents, to have a militia here, gangs here and there and an underground below, we won’t agree.”

The United States and European Union train and support Mr. Abbas’s troops in the hope of creating a strong enough force to prevent Hamas from challenging its West Bank rule and ultimately perhaps helping Mr. Abbas back into Gaza.

Hamas officials accused the West Bank authorities of collaborating with Israel and the West, and betraying the Palestinian national cause. Israeli officials pointedly declined to comment, not wanting to be seen by West Bank residents as being too closely tied to the Palestinian Authority. But Israeli soldiers control the West Bank, and Palestinian security forces coordinate their actions with them.

On Thursday in the south Hebron hills, Israeli security forces killed a long-wanted Hamas militant said to have been involved in planning two suicide bombings that were carried out against Israelis in the 1990s.

After Hamas, an Islamist group that rejects Israel’s existence, won Palestinian legislative elections in 2006, it and Fatah tried to put together a unity government. But tensions were high and street fights in Gaza between forces loyal to the two movements were common. Two years ago the skirmishes broke out into a four-day war, and Hamas took over Gaza entirely, leaving Fatah in power only in the West Bank.

Abu Obaida, a spokesman for the Hamas military wing known as the Qassam Brigade, said at a Gaza news conference on Sunday, “We are confronting two enemies, the Israeli occupier and the agency that serves the agenda of Washington and Tel Aviv.”

A Fatah leader in Gaza said some of his men had been arrested Sunday following the Qalqilya clash. Hamas leaders said that unless their men were released in the West Bank, unity talks would not proceed.

In other developments on Sunday, the Israeli cabinet rejected a bill aimed at Israel’s Arab minority that would have required a loyalty oath for citizenship. This means the bill, championed by the Yisrael Beiteinu Party of Foreign Minister Avigdor Lieberman, has little chance of passing in the Israeli Parliament. Lawmakers could still sponsor an independent bill on the issue, but it would not have the government’s backing.

A second bill from Yisrael Beiteinu that has been highly controversial was watered down by the cabinet. It was aimed at barring any commemoration of Israel’s Independence Day as Nakba Day, meaning the day that Palestinians suffered a catastrophe. Enacting such a ban was widely viewed as a violation of the country’s free speech laws. The ministers changed the draft of the bill so that it barred any possibility of spending public money to recognize Nakba Day. This version will still have to pass three rounds of voting in Parliament.

Israel started a five-day civil defense exercise on Sunday aimed at the possibility of coping with multiple missile attacks, the largest ever of its kind. The drill will involve staging mock disasters and testing emergency crews in their ability to evacuate buildings. On Tuesday, sirens will sound, requiring everyone to go into a secure space.

At the start of the Sunday cabinet meeting, Prime Minister Benjamin Netanyahu spoke of the drill and of the death on Saturday of Ephraim Katzir, who was president of Israel from 1973 to 1978 and a noted biophysicist at the Weizmann Institute. He was 93. “He was a rare combination of personal ability and public mission,” Mr. Netanyahu said.