Between July and September, 101,000 listeners tuned in, a drop of 2,000 compared to the previous three months, according to Radio Joint Audience Research (Rajar) figures.
Radio Wales increased its audience to 340,000, with 7,000 extra listeners.
BBC Wales has not commented on the figures.
Both stations attracted record low numbers of listeners during the second quarter of this year.
The editor of BBC Radio Wales has since stepped down, while Radio Cymru has launched a separate temporary service called Radio Cymru Mwy on some digital platforms.
Listening figures do not take account of catch-up listening or podcast downloads, although Rajar said more than 98% of listening still happened live.
In commercial radio, there were increases in audiences for Capital FM in south and north Wales, while Heart gained listeners in the south but lost listeners in the north.
The audience for BBC Radio Cymru has fallen to its lowest level this century - three months after its previous record low.