By TOM VANDEN BROOK

WASHINGTON — The Marine Corps whistle-blower who called out his service for not protecting its troops in Iraq with armored vehicles has reached a settlement with the Marines that allows him to keep his job and to help develop guidelines for those who raise concerns about internal wrongdoing, a federal agency announced Thursday.

Franz Gayl, a civilian science adviser and retired Marine officer, had been suspended, reprimanded and stripped of some of his security clearances after he went to Congress and the media, including USA TODAY, to raise alarms about urgent pleas for Mine Resistant Ambush Protected (MRAP) trucks. His concerns were brushed aside by his superiors.

“This resolution not only vindicates me but also my loyalty and dedication to the Marines, which never wavered,” Gayl said in a statement released by the Government Accountability Project, which represented him.

Gayl began advocating for MRAPs in 2006 while stationed in Iraq as a civilian science adviser. He saw the toll from roadside bombs on Marines in poorly protected Humvees and pushed for MRAPs to be fielded immediately.

At the time, improvised explosive devices (IEDs) caused up to two-thirds of the casualties suffered by U.S. troops there. He went outside the Pentagon, raising his concerns on Capitol Hill, where he found support from Sens. Kit Bond, R-Mo., and Joe Biden, D-Del.

Soon after, then-Defense Secretary Robert Gates, who had seen a story in USA TODAY about the effectiveness of MRAPs, made rushing the trucks to troops the Pentagon’s top priority. He and the Pentagon credit the vehicles with saving the lives of hundreds of troops.

Gayl’s criticism about the Marines’ failures to field MRAPs rapidly were affirmed by a Pentagon inspector general’s report released in 2008. The report found that Marine combat planners delayed for months an urgent request in 2005 for 1,169 MRAPs. Gayl has said his advocacy for MRAPs and other equipment made Pentagon and Marine Corps procurement officials uncomfortable.

The Marines put Gayl on leave with pay in 2010 after his security clearance had been suspended for alleged improper use of a flash drive in a secure computer. Gayl maintained he never used the portable data storage device, but the Marine Corps threatened to suspend him indefinitely without pay.

The U.S. Office of Special Counsel, which handled Gayl’s whistle-blower complaint, stepped in and mediated the settlement announced Thursday.

“I commend Franz Gayl and the Marine Corps for their hard work and willingness to negotiate in good faith towards a settlement that is satisfactory to both parties,” Special Counsel Carolyn Lerner said in a statement.

The Marine issued a brief statement: “The Marine Corps successfully resolved Mr. Gayl’s complaints through the U.S. Office of Special Counsel’s (OSC) mediation program. The U.S. Marine Corps does not normally discuss terms of such resolutions.”