From July to the end of September, an average of 384,000 people listened weekly to BBC Radio Wales, down 24,000.
BBC Radio Cymru saw its audience drop 12,000 to 104,000 in the same period.
A BBC Cymru Wales spokesman said: "As ever, we'll analyse these figures to ensure we continue to offer the best possible content for our audiences."
It was Radio Cymru's lowest recorded figure, a drop of 1,000 from this time last year. The Radio Wales figure was the station's lowest for six years.
In the commercial sector, some of the most popular stations in Wales saw increases in their weekly audiences.
Heart South Wales gained 94,000 listeners, up from 458,000 to 552,000.
Heart North Wales was up 7,000 to 136,000 listeners, while Capital South Wales was up 16,000 to 215,000.
But others saw falls. Juice FM, which broadcasts in north east Wales and Liverpool, was down 34,000 to 217,000, and Swansea Sound dropped 6,000 to 44,000.
The number of people listening to BBC Cymru Wales' national radio stations has fallen for the second successive quarter, the latest Rajar figures show.