JERUSALEM — The first of 1,000 United States troops have begun to arrive in Israel to take part in a joint missile-defense exercise, which the lead American planner described on Wednesday as the largest in the history of the two countries’ relationship and a testament to the strength of their military ties.

The planner, Lt. Gen. Craig A. Franklin of the Air Force, said the three-week drill, called Austere Challenge 2012, would be the sixth in a series of large-scale joint exercises and had been planned for more than two years. He called it a purely defensive drill unrelated to any specific developments in the region.

But it comes against the backdrop of tensions with Iran and persistent questions about whether Israel might strike the country’s disputed nuclear program. In addition, Republicans have sharply questioned the Obama administration’s commitment to Israel’s security during the presidential campaign.

Briefing reporters during a conference call from Ramstein Air Base, Germany, the headquarters of the United States air forces in Europe, General Franklin and his Israeli counterpart, Brig. Gen. Nitzan Nuriel, said at least 3,500 Americans in Israel and Europe and about 1,000 Israeli troops in various locations across the country would work as a team to prepare for the possibility of rockets, mortar rounds, and short-range and long-range ballistic missiles fired from multiple fronts.

According to the United States European Command, Patriot air defense batteries, an Aegis ballistic missile defense ship and related air defense systems will be deployed and integrated with Israeli equipment as part of an overall air defense network.

Israel’s Arrow 2 and Iron Dome missile-defense systems, developed with financing from the United States, will also play a role in the exercise, as will David’s Sling, a newer interceptor designed to tackle medium-range rockets and missiles. The exercise will mostly be based on computer simulations, but it will also include a live-fire exercise. The cost to the United States will total about $30 million; Israel’s total will be about a quarter of that.

Austere Challenge 2012 was originally scheduled for the spring, but General Franklin said it was postponed at Israel’s request. The Israeli foreign minister, Avigdor Lieberman, said in January that both sides had agreed to the postponement for “diplomatic and regional reasons,” citing regional tensions and instability.

The exercise has been modified to reduce the number of American forces in Israel, though General Franklin said that the scale of the exercise and total number of participants was essentially unchanged.

General Franklin said the drill was “not meant to send a particular message.” But General Nuriel said that “anyone who wants can get any message he wants from this exercise,” and that the fact that it was joint training mission was a strong message.

Israel has recently had to deal with new local threats. This month, it shot down a drone aircraft that entered Israeli airspace and flew 35 miles across the southern part of the country. Hassan Nasrallah, the leader of Hezbollah, the Lebanese militant group and political party, boasted that his fighters had assembled and piloted the drone, which had been designed in Iran.

In addition, Israeli defense officials said that Palestinian militants from Gaza had, for the first time, fired an antiaircraft missile at Israeli aircraft during cross-border violence last week. Officials said the missile, which missed, was probably a Strela shoulder-fired missile that most likely came from Libya.

Yossi Kuperwasser, who directs the Israeli Ministry of Strategic Affairs, said that weapons had been flowing into Gaza since the Libyan revolution toppled the government of Col. Muammar el-Qaddafi. Speaking to reporters in Jerusalem on Wednesday, he said that Israel had assumed for the last few years that Gaza’s militants had acquired a few antiaircraft missiles, but he said they had never been used before.

Mr. Kuperwasser said that he did not know which group in Gaza fired the missile, but assumed that a buildup of such arms there would ease any policies restricting their use.

In a rare sign of reassurance amid the regional tumult, Israel’s president, Shimon Peres, welcomed new ambassadors from Egypt and Jordan on Wednesday. Jordan has not had an ambassador in Israel in two years.

With Israeli-Egyptian relations all the more delicate since the election of the Muslim Brotherhood’s candidate, Mohamed Morsi, as president, Mr. Peres used the occasion to send a message: “I wish to convey to President Morsi my very best wishes for his success, for the success of Egypt and for the success of the Middle East.”