Israeli undercover troops broke into a West Bank apartment building in a failed arrest raid Thursday, igniting a violent protest and signaling that Israeli-Palestinian security coordination may be in trouble, officials said.

Thursday's raid targeted a suspected Islamic militant and marked the second time this week an army operation sparked clashes. Palestinians accused Israel of taking provocative actions in retaliation for their successful bid in November to win U.N. recognition of a state of Palestine in the West Bank, Gaza and east Jerusalem, the territories Israel captured in 1967.

Israel's military denied it was walking away from coordination with the security forces of Palestinian President Mahmoud Abbas, whose self-rule government administers just over one-third of the West Bank, where more than 90 percent of the Palestinians live.

Palestinian officials said Thursday's operation began when undercover troops, followed by uniformed soldiers in more than a dozen jeeps, broke into an apartment building on the outskirts of the West Bank town of Jenin. The apparent target, an activist in the militant Islamic Jihad group, was not in the area.

The Israeli military said several hundred Palestinians began throwing stones, and that some in the crowd hurled firebombs and rolled burning tires toward the soldiers. Troops fired warning shots, and also used tear gas, stun grenades and rubber-coated steel pellets to quell the protest, the military said.

Talal Dweikat, the Palestinian governor of the Jenin district, put the number of stone throwers at several dozen. He said a Palestinian was shot in the leg and an elderly woman was bitten by an army dog. The military confirmed a woman was bitten and taken for medical treatment.

In recent years, the West Bank has been relatively calm, in part because of Israeli-Palestinian coordination in tracking Islamic militants. The coordination came in response to the 2007 takeover of Gaza by the Islamic militant Hamas, Abbas' main political rival.

Trying to prevent a similar takeover in the West Bank, Abbas began cracking down on Hamas and found his interests aligned with Israel's. Abbas has long argued that violence is counterproductive, since Palestinians are bound to lose any armed confrontation with Israel. Hamas believes Israel will make concessions only in response to force.

Security coordination with Israel is unpopular in the West Bank, especially at a time when peace talks are frozen and Palestinian independence appears unlikely anytime soon. U.N. recognition gave the Palestinians a diplomatic boost but changed little on the ground.

Palestinian officials alleged Thursday that the recent Israeli raids are part of Israel's retaliation for the statehood bid. Israel strongly opposed the U.N. recognition, saying it was an attempt to bypass negotiations.

A Palestinian security official said Abbas has ordered his security forces to avoid any confrontations with Israeli troops. Abbas is concerned about an unwanted escalation he believes will not serve Palestinian interests, said the official who spoke on condition of anonymity because he was not authorized to discuss internal deliberations with reporters.

Adnan Damiri, a spokesman for the Palestinian security forces, said Israeli troops have increasingly entered Palestinian-run areas without coordination since November. "There has been an escalation in Israeli raids into our territories since the U.N. bid," he said.

Earlier this week, another undercover raid targeting suspected Islamic Jihad militants in the West Bank prompted clashes that left 10 Palestinians wounded.

Lt. Col. Avital Leibovich, an Israeli army spokeswoman, said Israel has not abandoned security coordination with the Palestinians. "As far as we are concerned, the coordination has not changed," she said. "Our activities are in relation to threats (by militants), and nothing else."