A spokesman for Arts, Culture and Heritage Minister Chris Finlayson said the act was "disgusting''.
Details about what had happened were still unclear at this stage because the Ministry did not have a representative in the area. Further information would come from the CWGC.
Khaled Al-Jazwi, a spokesman for the Benghazi local council, told the Guardian the attack occurred on Thursday.
"We don't know yet who did this. We have spoken to the local council's security committee about investigating who is behind this. This cemetery has been here for decades and nothing like this has ever happened before.''
The CWGC was still in the process of replacing or repairing graves damaged in the March attack.
The 11 New Zealanders buried in at the Benghazi War Cemetery are: Private Hedley James Boult, Flying Officer Hector Hugh Crawford, Flight Sergeant Lorenzo Richard Feasey, Flying Officer William Lynn Kauter, Lance Corporal Arthur Leslie Milne, Sergeant Maurice Reginald Mutton, Lieutenant Hector Alexander McAulay, Flight Sergeant Mitchell Ridland, Aircraftman First Class Thomas Martin Scott, Pilot Officer William George Duncan Thurston, Private Peter Edgar Alfred Vivienne Wardle.
Libyan authorities have apologised for the March desecration.
Some 1214 Commonwealth troops who died in the north African desert battles of World War II are buried at the Benghazi War Cemetery.