This year’s Peabody Awards hold special places of honor for independent producers, just as critics charge PBS is trying to marginalize them.

Operating with far fewer resources than the PBS network, independent producers won four awards, while their wealthier PBS colleagues won three.

The series “Independent Lens” was the only television program honored with two Peabodys, both for documentaries – one award went to “Bhutto,” on the life of Benazir Bhutto, described by ITVS as “an epic tale of Shakespearean dimension. It’s the story of the first Muslim woman elected in history to lead an Islamic nation: Pakistan.” She was assassinated in 2007 by extremists as she campaigned for another term in office.

“Who Killed Chea Vichea?” was the other “Independent Lens” documentary honored, and it too profiled a leader who was killed in public, Cambodian union president Chea Vichea.

Two other Peabody Awards were won by independent producers working with American Documentary , one for the documentary “My Perestroika” and another for StoryCorps, shared with NPR for programs on the tenth anniversary of 9/11.

The other three public television winners were for programs on “American Experience,” presented by WGBH in Boston; “American Masters,” presented by WNET in New York, and “Austin City Limits” from KLRU-TV in Austin, Texas.

The honors for independent producers came after PBS was criticized for reducing the audience for both “Independent Lens” and “POV” by shifting both series to Thursday nights, which have historically been reserved for PBS stations to present their own local programs. And on Thursdays, many stations program comedy reruns, which are less compatible with documentaries than other public TV programs. Those have contributed to a loss of almost half of the audience for those independent documentaries, according to a report in Current magazine.

Even PBS considered Thursdays are a “no-fly zone,” as John Wilson, the network’s chief programmer, described that night in a meeting with reporters. Wilson was also quoted in Current as promising to “review the results of the year-round, weekly slot Thursdays at 10 p.m. and consider other scheduling options for fall 2012 and beyond.”

PBS’ action resurrects a decades-long dispute about the network’s treatment of independent producers. Indeed, ITVS itself was funded by Congress because of complaints independent producers were not being welcomed at PBS.

“In 1988, Congress mandated the creation of a service dedicated to independently produced programming that takes creative risks, sparks public dialogue, and gives voice to underserved communities,” according to the ITVS web site.

One prominent critic of PBS’ scheduling of independent documentaries is longtime PBS host Bill Moyers. Last month Moyers took his complaint public, urging PBS to support documentaries by “reversing a bad decision and returning to a national core time slot the independent documentaries created — often at real financial sacrifice — by the producers and filmmakers whose own passion is to reveal life honestly and to make plain, for all to see, the realities of inequality and injustice in America.”

Moyers also invited supporters to sign a petition urging PBS to return independent films to a more favorable time.