The UN-backed tribunal's 250 local workers, including judges and prosecutors, have not been paid since June because of a cash shortage. Most of them have been on strike since September 1.
UN spokesman Lars Olsen said in an emailed statement that the world body had successfully worked with major donors to secure their authorisation to make a further loan to the Cambodian side of the court for "the payment of arrears of national salaries".
"We hope that the national staff of the ECCC will now be able to return to work on this basis," he said.
The UN also called on Cambodia to "meet its obligation" to pay salaries for the national staff.
"Any further strikes could risk delaying the judicial proceedings and jeopardise the court's ability to function," Olsen added.
Neth Pheaktra, a Cambodian spokesman at the tribunal, said the striking staff were expected to return to work on Thursday.
The hybrid court has been frequently short of cash since it was set up in 2006 to seek justice for the deaths of up to two million people under the brutal communist Khmer Rouge regime in the late 1970s.
The court was forced to suspend proceedings for about two weeks in March due to a strike over unpaid wages.
Two defendants - "Brother Number Two" Nuon Chea, 87, and former head of state Khieu Samphan, 82, are on trial for war crimes, genocide and crimes against humanity.
The court is currently in recess and preparing to hear closing statements in the first part of the trial in mid-October.
The tribunal which has been dogged by allegations of political interference suffered a new setback last week with the resignation of a key prosecutor, the latest in a string of departures from the trials of former Khmer Rouge leaders.
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