A new primary school built for 420 pupils is currently home to only 180, due to a planning row involving the home of moles and voles.
The rest of the children are having to remain in the old school, half a mile away.
Plans for a road to the new St Philip and St James Cof E primary in north Oxford have run into opposition. Residents want land it would cross - which is home to moles, voles, badgers and lizards - designated as a "town green".
The case goes before the High Court in July.
Meanwhile, the only way to reach the new school is via a single-track hump-back listed canal bridge. Planners have placed a limit on the number of children allowed to use it on their way to school because of safety fears. As a result parents have to drop children nearby allowing them to walk across or take them to the old school site to catch a bus.
The duplication involved is putting pressure on the school's budget and burdening staff. PE equipment shared by the two schools has to be ferried across the sites.
Irene Conway, the head, said: "The children have got more room on both sites and are enjoying that. We are all very positive and the staff are working as a team. We are here to make sure the children enjoy coming to school and are learning and achieving as much as they can.
"But for the parents, it is very difficult. We are almost like an infant and junior school. Parents with children in both age groups cannot be at both sites. It has caused a lot of consternation and difficulty."
Sebastian Rahtz, a parent governor, said the governing body had asked Oxfordshire council's planning committee to allow all the children to attend the new school, subject to safety measures.
But if that compromise is rejected, he fears the school will continue to be housed on two sites for two or more years while the access road dispute is resolved.
Sally Presdee, the school's chair of governors, said: "The school is doing really well, but we feel we have been let down. Some bright spark suggested we build the school on this site, and in 1999 when the whole process started, you would have thought it was plain we needed the road - yet it was just left. The city council said the county would sort it out and vice versa."