TEL AVIV, Israel — The Pentagon’s Missile Defense Agency (MDA) will manage two separate airborne missile-tracking sensor programs, one self-initiated in support of U.S. missions and the other a congressionally directed joint development with Israel.

Both programs — the U.S. Airborne Infrared (ABIR) and the Israeli Airborne Early Warning Sensor (ABEWS) — involve very long-range ballistic missile sensors deployed on high-flying drones. And both, U.S. and Israeli officials say, will enhance the ability to track large ballistic missile raids and distinguish countermeasures and decoys from real incoming warheads.

But while conceptually similar, the parallel programs are operationally distinct, with ABIR designed for rapid scrambling anywhere in the world in support of U.S. intercept missions while ABEWS will fly safe and high — some 12,000 meters — within Israeli airspace for round -the-clock discrimination duty during wartime or periods of political tension.

“There are differences in our fundamental approach that I cannot get into due to classification sensitivities,” said U.S. Army Lt. Gen. Patrick O’Reilly, MDA director. “We are not refuting why Israel desires what they are looking for and we agree that the concept would be applicable to that part of the world and the particular geometries that Israel has to deal with. But our requirements are clearly different.”

When pressed to explain, O’Reilly said: “We need to build systems that are truly adaptable and can be quickly surged. We need the ability to redeploy; to put a lot of capability out quickly to address crises, as they occur, because we cannot afford to have constant missile defense around the world.”

For nearly three years, Israel has pitched for joint funding of new drone-deployed infrared sensors to track ballistic missile salvo strikes and distinguish their countermeasures and decoys from real incoming warheads. The proposed ABEWS is viewed here as an essential support element of future Block 5 versions of the Arrow Weapon System, which is slated for initial deployment before the middle of the decade.

But following an extensive review, MDA officials determined that a persistently deployed system — while valid for defending Israel against Iranian missiles — would not meet U.S. needs for a more versatile system rapidly deployable against a full spectrum of threats worldwide.

Under MDA’s revised, phased adaptive plan for European and homeland defense, the Pentagon is moving forward with a U.S.-only airborne infrared, a forward-based unmanned sensor that tracks large salvos of incoming ballistic missiles and discriminates actual warheads from decoys and other countermeasures. MDA is seeking $47 million in 2012 to integrate a prototype sensor on an MQ-9 Reaper drone for demonstration purposes, pending a long-term acquisition and deployment strategy.

In parallel, MDA will support integration of Israel’s own drone-deployed sensor out of existing U.S.-Israel Arrow Weapon System cooperative funding, but not as a separate budgetary line item for a new joint development program. In language accompanying the Pentagon’s budget for 2011, Congress directed MDA to support joint ABEWS development, and MDA “is fully complying with this direction,” O’Reilly said.

Program officials from both countries are discussing the exact scope and cost-sharing formula for the joint effort, since Congress did not appropriate a specific amount for ABEWS. Instead, lawmakers prescribed that a portion of funding appropriated as part of the Long Range Detection Suite, or LRDS, be earmarked for ABEWS.

“It appears to be left to the parties to determine how much of the plus-up will be for LRDS activities,” said MDA spokesman Rick Lehner.  “Representatives of both governments are currently discussing the scope of LRDS efforts, of which ABEWS is a part.”

ABEWS is an operational follow-on to a six-year prototype development between Israel and Germany code-named Blue Bird. Under that project, which concluded in late 2009, partners tested a long-range infrared sensor on a manned business jet platform and presented relevant data to MDA for analysis.

While details of ABEWS remain sensitive, defense and industry sources say it consists of a long-range, high-resolution infrared detection sensor developed by Rafael Ltd. and deployed on Israel’s newest, largest, long-endurance Eitan drone, built by Israel Aerospace Industries. The unmanned infrared sensor would support existing Elta-developed Green Pine and Super Green Pine L-band fire control and tracking radars, as well as the U.S. AN/TPY-2 X-band early warning radar based in Israel’s Negev desert.

In addition to the improved precision tracking from a blend of infrared and radar sensors, ABEWS aims to discriminate between actual, possibly nuclear-tipped warheads  and the dozens of decoys and countermeasures that threaten to confound national missile defenses, sources here say.

“A few years ago, many in MDA believed it was not a valid technical solution. But today, it is proven. There are no physical constraints, and now everybody’s convinced it will work,” Arieh Herzog, director of the Israel Missile Defense Organization, said in an interview last year.

In an April interview, Herzog reaffirmed Israel’s commitment to deploy ABEWS as part of future Block 5 versions of the Arrow Weapon System, which integrates the planned Upper Tier Arrow-3 and existing Arrow-2 interceptors into a single national missile defense system.

As for the parallel U.S. program, MDA budget documents for 2012 describe ABIR as “a forward-based sensor to provide the capability to track large ballistic missile raids, decreasing the time between the enemy’s launch of the first ballistic missile and the first launch of a ballistic missile interceptor.” MDA initially requested $112 million in 2011 for ABIR, not only for integration of an infrared sensor but to purchase airframes for use beginning in 2015.

Over the past year, however, MDA opted to reduce funding for ABIR, requesting $47 million to integrate an infrared sensor on a Predator-B drone by San Diego-based General Atomics. “Rather than purchasing airframes, we intend to integrate a sensor from the Multi-spectral Targeting System family of [infrared] sensors onto an MQ-9 Reaper … to prove that we can close the fire control loop with a forward-based airborne asset,” MDA said in its 2012 budget book presented to Congress this year.

According to the MDA document, ABIR and the planned Precision Tracking Space System  are designed to enhance Washington’s so-called Phase 3 Robust IRBM intermediate-range missile defense scheduled for completion in 2018 as well as the Phase 4 Early Intercept and Regional ICBM Defense planned for deployment by 2020. “[Precision Tracking Space System] sensors in space will detect and track hostile ballistic missiles and enable earlier engagements to improve both homeland and regional defense,” noted MDA authors, while ABIR marks “another potential enhancement,” particularly in so-called raid or salvo strike scenarios.