The future of the Little Branches nursery in Govan is "unclear" following news its intake from next year would be reduced from 36 to 16.
Glasgow City Mission may be unable to operate the centre, which has been running for more than 20 years, with so few children.
The charity's boss disputes Glasgow City Council's claims, which we reported yesterday, that the changes to funded nurseries are due to facilities not meeting the standard in recent inspections.
Writing to the Evening Times, chief executive of Glasgow City Mission Grant Campbell, said: "In light of such positive feedback, we would invite Glasgow City Council to revise its comment as to why 20 places have been withdrawn from Little Branches Nursery.
"In the interim, we would like to assure families in Govan that we are currently working hard to try and resolve this situation in a way that honours the children, families, volunteers and staff."
Mr Campbell also said the "devastating news" means that "the viability of the centre is at present unclear."
As reported in yesterday's Evening Times, nurseries across the city discovered their funding was to be withdrawn completely or reduced. The city council said some did not meet the standard they required and added that places in the affected areas would not be reduced.
They also said some of the nurseries, which includes Little Branches, did not come out top in the tendering process for places which is assessed based on quality, the provision of extended hours and links to further education.
Little Branches' latest review by the Care Inspector-ate achieved a score of 'very good' across all nine points.
A city council spokeswoman said officers will meet with nursery staff today, and added: " Little Branches came second in the procurement process so the places went to the facility which ranked first.
"These are private nurseries and cannot rely on partnership places so they have to look for business elsewhere."
Clarence House, in the West End, and facilities in the South Side and Cardonald, are also affected by the funding withdrawal.