Yes it is. I just rang the surgery when H left and told them my son was now called by my maiden name - they just changed it, no questions asked.
But for any legal documentation - passport, etc, DCs will have to have the full surname if it is on their birth certificates, which it sounds like it is.
My exH's daughters by his ex-P had a double-barrelled surname and they have always only been known by one of the surnames only. (Except for passports and..later..mortgage applications nd circs where you have to produce their birth certificates as compulsory proof of ID)
You might want to consider though whether it is the girls' long-term interests to have this name confusion. How old are they and if old enough, what do they call themselves?
And whether we like it or not, he is their father and they may, later in life, have wanted to retain the name.
I did not have to consider those questions much as ds was 6 monthds when his father fecked off abroad and has never been in contact since. He knows himself by my maiden name and i am in process of getting a changev of name order to make it official so I can get his passport changed.
If your ex agrees to a change of name order you can change it officially - but would your ex-p agree? It costs 175 quid to go to court for the order.
HTH