Thousands of unsupervised children would be forced to cross light rail tracks along the eastern suburbs extension each day on their way to school, bringing "real possibilities" of fatal accidents, according to evidence presented to planning authorities.

The $2.1 billion eastern suburbs light rail project may also cause road traffic to bank up behind trams, and even generate electromagnetic interference that could jeopardise equipment at a nearby cancer research facility, public submissions lodged in December said.

Major construction of the light rail line, from Circular Quay to George Street through Surry Hills to Randwick and Kingsford, is due to start in April.

Transport for NSW has proposed changes to original light rail plans approved in June, such as downsizing a light rail stop at Moore Park, removing the proposed World Square stop and introducing 67-metre vehicles which would run less often than originally planned, but carry more passengers.

But in evidence to planning authorities, groups representing Sydney Girls and Boys High schools, both at Moore Park, say the changes will force a "surge of school children" to cross the tracks by foot during the morning and afternoon rush.

An elevated concourse has been removed from plans for Moore Park station, meaning it no longer connects to a proposed overhead bridge crossing Anzac Parade which would have linked to the schools. An underground pedestrian subway will be built, but would only open on special event days and not for school students.

"Injury even death are real possibilities," resulting from the change, the Sydney Boys High school council said, foreshadowing "serious accidents", especially if children dashed across the tracks to catch a departing tram.

A group representing the Sydney Girls High School community said about 2000 children would cross the tracks unsupervised in a short space of time, potentially putting them on a collision course with light-rail vehicles.

A Transport for NSW spokeswoman said the stop's design was changed to fit in with surrounding parkland, and would be "accessed safely via a pedestrian crossing over light rail tracks".

The University of NSW has 50,000 students and staff and would be serviced by two of the busiest stops. It said transport authorities had not consulted adequately nor properly considered threats to safety, traffic flow and university operations, despite some concerns being repeatedly raised.

The longer vehicles are expected to increase passenger capacity by 55 per cent, but the university expressed concern that transport authorities have not considered how platforms will cope with the extra load.

It said crowds of passengers may try to cross Anzac Parade against the signals, or traffic would be forced to wait for longer periods.

The university said the recently constructed Lowy Cancer Research Centre was located within 25 metres of a proposed stop, and light rail had been known to cause electromagnetic interference which could affect scientific and medical research equipment.

If the research was jeopardised, the facility would be forced to relocate or be lost to another university, the submission warned.

The City of Sydney cautioned against a potential overflow of passengers onto footpaths and longer pedestrian wait times in the city, saying the issues "have not been adequately explored".

Randwick City Council noted that the modified plans had only been exhibited for two weeks, and would result in the loss of significant trees in Centennial Park and increased noise impacts.

Fairfax Media has previously revealed that costs for the light rail project had blown out from $1.6 billion to $2.1 billion.

A Transport for NSW spokeswoman said it would examine the concerns raised, adding that consultation "has been central to the light rail project" and the department would work with the University of NSW to mitigate impacts on sensitive equipment.

"Light rail will improve the whole transport network and reduce congestion by taking around 220 buses off the road," she said, adding that traffic light programming would assist pedestrians.