A Govan nursery has also been forced to close after the council withdrew funding for 20 places, making it impossible to keep the centre open.
The Little Branches facility, in St Kenneth Drive, shut its doors yesterday after receiving the "devastating news" earlier this week.
Grant Campbell, the chief executive of Glasgow City Mission, which runs the nursery, said despite the council offering to pay for 16 places "the reduction was too much of a financial hole for us to fill and we had to make the decision to close".
A council spokeswoman said: "We are disappointed this decision has been taken and we will work with the parents to find alternative provision."
Local people have been left upset and angry by the move, and are understood to have met Govan Councillor James Adams last night in an attempt to resolve the problem.
The council said the facility did not come top in the legal tendering process and so it could not continue to fund all 36 places.
Clarence House Nursery, in the West End, has not been offered any paid places by the council, and has had all of its partnership funding removed.
Parents are fuming over the decision, which they say is forcing them to move their child or pay up to £1000 a term in childcare fees.
Maureen Cox, whose son Joshua, 3, attends the nursery in Hotspur Street said: "I know so many children who have fond memories and wonderful experiences of Clarence House. Joshua is very happy there.
"I am disappointed and angry for our son that even though the Government says it offers free sessions for his two pre-school years they are willing to damage his development, friendships and education or leave the family with very little money.
"It's taking away parental choice."
Nursery staff are planning to launch an appeal.
The council says Clarence House came fourth in the procurement process and so the facility was not offered any payment.
Parents whose children attend Happitots Nursery in Bishopbriggs have also started a petition after East Dunbartonshire Council removed funding.
The council says it "followed the required legal and procurement procedures" when awarding the partnership contracts and nursery bosses are understood to be in meetings with the local authority.