The Pentagon announced it will close three Air Force bases in Britain as well as more than a dozen smaller installations in Germany, Belgium, the Netherlands and Italy. (AFP/Getty Images)

The Pentagon will close three Air Force bases in Britain that date to World War II as part of a broad realignment of U.S. forces and installations throughout Europe, defense officials announced Thursday.

Over the next six years, the Air Force will leave RAF Mildenhall in Suffolk — home to Special Operations forces and aerial refueling tankers — and close key intelligence analysis centers at RAF Molesworth and RAF Alconbury, two smaller adjacent bases in Cambridgeshire.

Most of the roughly 5,000 personnel at the three bases will be transferred elsewhere in Britain and to other installations in Europe, but the closures will result in an overall reduction of about 2,000 U.S. troops and civilian employees in the United Kingdom.

To cushion the blow, U.S. officials said they will base two squadrons of F-35 Joint Strike Fighters at RAF Lakenheath in Britain, the first U.S. deployments of the advanced fighter jets in Europe. Lakenheath is about five miles from Mildenhall and will add about 1,200 U.S. troops.

The Pentagon also will close more than a dozen smaller installations in Germany, Belgium, the Netherlands and Italy. Most are minor barracks, commissaries, camps and other sites. Along with the base shutdowns in Britain, they are collectively expected to save the Defense Department about $500 million annually, defense officials said.

All told, the U.S. military has about 67,000 troops stationed at bases in Europe, a number that is expected to remain about the same in the coming years.

“European and trans-Atlantic security is more important than ever,” Derek Chollet, the assistant secretary of defense for international security affairs, told reporters. “Yet at the same time, we must ensure that we pursue these goals in a way that is as efficient and effective possible.”

The United States leases Mildenhall, Molesworth and Alconbury from the Royal Air Force, and the properties will be returned to Britain after they are vacated.

U.S. military personnel at Molesworth and Alconbury — which provide intelligence analysis for the U.S. European Command, the U.S. Africa Command and the Defense Intelligence Agency — will transfer to an expanded $300 million intelligence hub at RAF Croughton, another U.S.-leased base in Britain.

Michael Fallon, the British defense secretary, said his government is disappointed by the U.S. decision to leave Mildenhall but cheered the announcement to base the F-35 fighters at Lakenheath. Britain has plans to buy about 48 of the U.S.-made stealth fighters and will base most of them at RAF Marham in Norfolk.

“This resounding vote of confidence by the U.S. is great news,” Fallon said in a statement. “Our historic relationship with the U.S. remains as strong as ever, and their decision to base their first European F-35 squadrons in the U.K. clearly reflects the closeness of our partnership.”

The F-35 is billed as the most advanced fighter jet ever built, and the weapons program is the most expensive in U.S. history. Many years in the making, the F-35 program has suffered developmental setbacks and cost overruns. The U.S. Marine Corps is scheduled to begin flying the F-35 operationally this year, followed by the Air Force next year and the Navy in 2018.

Lockheed Martin, based in Bethesda, Md., manufactures the F-35. The Pentagon plans to buy more than 2,400 of the fighters, and U.S. allies are expected to purchase several hundred more.