British Cycling and Sport England have lodged joint objections to new plans for the velopark after the London 2012 Games.
The changes, contained in two planning applications submitted by the Olympic Park Legacy Company (OPLC), are aimed at freeing up green space for Olympic Park residents while containing a new 1.6km long cycle route to a hub including the 2012 velodrome and the BMX park.
The two key sports organisations have raised technical and design queries about the loop of the cycle circuit.
It was originally meant to cut across the River Lea but the OPLC want to switch the loop to a spot along the north east of the Olympic Park near the BMX venue.
Planning rules state any new route must cover the same distance, difficulty, rise and fall and be delivered to the same deadlines as originally earmarked.
In a joint statement British Cycling and Sport England said: “We believe the existing plans for the velopark approved by the ODA (Olympic Delivery Authority) will ensure a greater legacy for cycling following London 2012 and are fully supported by the key project partners including British Cycling and Lea Valley Regional Park Authority.
“While the objection has been lodged, we are trying to work with all parties involved in the velopark to find a satisfactory solution to the issue.”
Under current plans the cycle circuit, including a 6.5km mountain bike trail, is to be added to the site after the Games and to be open by 2014.
The velodrome and BMX are to be open by 2013.