The couple who guided a four-star general

Frederick and Kimberly Kagan, a husband-and-wife team of hawkish military analysts, put their jobs at influential Washington think tanks on hold for almost a year to work for former General David Petraeus when he was the top US commander in Afghanistan. Given top-level security clearances in Kabul, they pored through classified intelligence reports and participated in senior-level strategy sessions to advise Petraeus about how to fight the war differently. And in the end, they were able to change the US strategy in Afghanistan.

Their compensation from the US government for their efforts? Zero dollars. Although Fred Kagan said he and his wife wanted no pay in part to remain "completely independent", the extraordinary arrangement raises new questions about the access and influence Petraeus accorded to civilian friends while he was running the Afghan war.

Petraeus was recently forced to step down as director of the CIA amid a scandal involving his extra-marrital affair with his biographer Paula Broadwell, whom he also allowed to read sensitive documents and accompany him on official trips.

But the access granted to the Kagans, whose think tank work has been embraced by Republican politicians, went even further. The general made the Kagans de facto senior advisers, a status that afforded them numerous private meetings with him, priority travel across the war zone and the ability to read secret transcripts of intercepted Taliban communications, according to current and former senior US military and civilian officials.

The Kagans advocated substantive changes in the US war plan, including a harder-edged approach than some officers advocated in combating the Haqqani network, a Taliban faction in eastern Afghanistan, the officials said.

The pro-bono relationship, which is now being scrutinised by military lawyers, yielded benefits for the general and the couple. Defense contractors had an incentive to contribute to Kim Kagan's think tank. While Petraeus's closeness to two analysts respected by the Republicans helped to shore up support for the war among Republican leaders on Capitol Hill.

Fred Kagan said the arrangement was "uncomfortable" at times: "We were going around speaking our minds, trying to force people to think about things in different ways and not being accountable to the heads [of various departments]."

The extent of the couple's involvement in Petraeus's headquarters was not known to senior White House and Pentagon officials involved in war policy, two of those officials said.

On 8 August 2011, a month after he relinquished command in Afghanistan to take over at the CIA, Petraeus spoke at the Kagans' Institute for the Study of War's first "President's Circle" dinner, where he accepted an award.

"What the Kagans do is they grade my work on a daily basis," Petraeus said. "There's some suspicion that there's a hand up my back, and it makes my lips talk, and it's operated by one of the Doctors Kagan."

Petraeus declined to comment on this article.