WASHINGTON _ Defense manufacturing in New England is largely spared cuts in the Pentagon’s new budget proposal out today, with shipbuilders, helicopter firms, and missile makers in line to receive new orders – and in some cases even greater investments than last year.

However, modest cuts in defense research could have a ripple effect at some universities and smaller tech firms across the region that depend heavily on research grants and government seed money to pursue scientific breakthroughs.

The military’s research and development budget will fall from $71 billion last year to $69 billion, continuing a downward trend in recent years, possibly impacting projects funded by all the military branches:

-- The Navy’s research spending, which also finances the Marine Corps, will drop from $17 .9 billion to $16.8 billion;

-- The Air Force will go from $26.5 billion last year to $25.4 billion; and

-- The Amy’s research funding will remain roughly the same at $8.9 billion, though it will cut its investment in basic and applied research, the earliest stages of cutting-edge development.

Nevertheless, Pentagon budget documents insist that the spending plan “largely supports university basic research,’’ the first stage of cutting edge development even if it cuts other research areas.

The impact of cuts in the research budget could also be offset by new investments in other high-tech areas such as cyber security. For example, the Pentagon will increase overall spending on cyber defense by $3.4 billion, the documents show. That could be a boon for Hanscom Air Force Base in Bedford, which is home to the service’s Electronic Systems Center. Indeed the Air force budget alone for cyber programs is $4 billion, though the budget documents made available so far provide little insight into what the cyber investments are for.

Described as a “more disciplined use of defense dollars,” the Pentagon spending plan totals $613.9 billion for the fiscal year beginning October 1 -- including nearly $89 billion to cover war operations. That is down from a war budget of $655.9 billion this year.

With the withdrawal of US troops from Iraq last year and fewer ground forces expected to be fighting in Afghanistan, the proposal is also designed to support a new strategy that places greater emphasis on Naval and Air forces.

So while the budget will slash the size of the active-duty Army by 72,000 to 490,000 soldiers over the next five years and make some personnel cuts in other branches of the military, it is mostly good news for New England-based defense manufacturers that specialize in shipbuilding and aerospace. Here is a snapshot:

-- General Electric Aviation in Lynn is poised to build the engines for 26 new F/A-18 Super Hornet fighter jets for the Navy, just two less than last year, for a total of $2.1 billion. It will also see a modest increase in funding for research into aircraft upgrades. Meanwhile the Navy will once again next year purchase a dozen EA-18G Growlers, a version of the aircraft specially designed for detect and jam hostile missiles and aircraft – the same number as last year.

-- General Dynamics in Taunton, the prime contractor for the US Army’s Warfighter Information Network-Tactical, a communications network designed to link soldiers on the battlefield, will see a significant increase in investment. The budget request for the program is up nearly $162 million from last year to more than $1.2 million.

-- Waltham-based defense giant Raytheon will see some of its key weapons programs shielded from cuts and in some cases will get a boost.

For example, Raytheon is expected to share with other large firms the nearly $10 billion in continued investments in the nation’s ballistic missile defense program, including missile interceptors for Navy ships that are built by the company’s Tucson, Arizona, facility.

Raytheon is also set to build a new so-called X-band radar for the Army and Navy at a cost of nearly $600 million, the budget proposes.

Investments in missiles the company builds for a variety of attack planes and ships will grow substantially next year. The company builds the Advanced Medium Range Air-to-Air Missile, which will see an increase from $389 million to $423 million; the Air Intercept Missile-9x, which would get $200 million versus $150 million last year; and the Joint Standoff Weapon will also see a modest increase of $6 million to $133 million, the document show.

The company’s Small Diameter Bomb, designed for fighter and bomber aircraft, would also be increased from $182 million this year to $216 million in the new budget proposal.

At the same time, purchases of the so-called Evolved Seasparrow missile, built for the US Navy, will increase modestly as well, for a total of $58 million. The company’s Standard missile, designed for naval air defense, would receive $463 million, up from $403 last year, while the budget for the Tactical Tomahawk missile that is fired from ships at ground targets will increase from $306 million to $360 million.

Most of the projects that support helicopter production lines in Connecticut are protected in the budget. For example, Sikorsky Aircraft in Stratford would see orders for 59 new Black Hawk helicopters for the Army for more than $1.3 billion. While that is 13 fewer than was ordered this year, the Army plans to increase research on potential improvements to the transport helicopter from $8 million this year to more than $83 million.

The Stratford plant is also set to build 37 more versions of the venerable utility bird for the Navy for an additional $1.3 billion, according to the budget proposal.

Submarine maker General Dynamics in Groton, meanwhile, will get $4.2 billion to build a pair of Virginia-class attack submarines, the same as last year, though the budget will delay by several years start-up work on a new class of nuclear-armed submarines.

Meanwhile, aircraft engine maker Pratt & Whitney in Hartford will see continued production of the new F-35 fighter jet for the Air Force, Navy, and Marine Corps. The Pentagon plans to build 29 next year, versus 31 this year.

General Dynamics’ shipyard in Bath, Maine, is set to get orders for two Aegis class destroyers for the Navy, up from one last year, for a total investment of $3.5 billion.