Mid-ranking regime cadres Meas Muth, an ex-navy commander, and Im Chaem, a female former district official - both believed to be in their seventies - were charged in absentia by international co-investigating judge Mark Harmon, the court said in a statement.
It was the first time Muth and Chaem have been publically named as suspects by the tribunal, despite having been under investigation for some time.
But a Cambodian judge also on the tribunal did not sign off on the charges against the two suspects, reflecting wider unease over the reach of any fresh probes into a regime that massacred up to two million Cambodians in the 1970s.
Critics also claim strongman Prime Minister Hun Sen - himself a former regime cadre - is attempting to thwart the trials of lower level cadres.
The prime minister has repeatedly said that the current case against former top regime leaders would be the last.
So far only three people have been convicted by the hybrid tribunal, which was set up in 2006, including life sentences for the two most senior surviving Khmer Rouge leaders handed down last year.
"Decisions on whether these cases will end up with indictments or dismissals are expected next year," said court spokesman Lars Olsen.
Led by "Brother Number One" Pol Pot, who died in 1998 without ever facing justice, the Khmer Rouge dismantled modern society in Cambodia in their quest for an agrarian Marxist utopia.
In its historic debut trial, the court in 2010 sentenced former Tuol Sleng prison chief Kaing Guek Eav, alias Duch, to 30 years in prison - later increased on appeal to life - for overseeing the deaths of 15,000 people.
Their two-year trial focused on the forced evacuation of Cambodians from the capital Phnom Penh into rural labour camps as well as murders at one execution site.
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