Operators behind the initiative said large numbers of bikes are being dropped off in the Canonmills, Victoria Quay and Leith Links areas of the city, which are nearer sea level.
There are now plans to bring electric assisted cycles to the hilly city later this year.
By springtime, the firm is expecting to have 80 stations in place throughout Edinburgh in the build-up to an anticipated busy debut summer season.
Since launching in September, the initiative has provided almost 20,000 rides and has 49 stations around the city.
But there has been an increase in the number of bicycles appearing on social media that have been dumped in locations such as rivers, playgrounds and bushes - particularly in the north of the city.
Operator Serco has revealed that 100 bikes have been reported abandoned in the past five months with the vast majority being recovered.
At least 25 cycles have been seriously damaged while a total of ten have also been stolen in this time leading to police investigations.
Serco said the level of vandalism being experienced in Edinburgh is comparable to its other locations including London and Trondheim and Bergen in Norway.
Just Eat Cycles general manager Charles Graham said: “Our priority is to minimise the effect any anti-social behaviour has on users and we are confident that the new measures we are putting in place, including the relocation of some stations, will significantly reduce this type of behaviour. We’re working with Police Scotland to prosecute those responsible, and with the vast majority of stations covered by CCTV, we will catch those responsible.”